What the textbooks (except, of course, this textbook) don't tell you about the Northern and Southern Courts:

First, let us give credit to an historian who pointed out these matters in detail: Higuchi Kiyoyuki 樋口清之. See Chapter 5, "Naze, Nanbokuchō no sensō wa hyakunen ijō mo tsuzuita no ka?" (Why did the war between the Northern and Southern Courts continue for over 100 years?) in Himitsu no Nihonshi 秘密の日本史, (Tokyo: Yōdensha, 1988), pp. 45-51. Much of the raw factual information below comes from this book, though Higuchi--a vigorous cultural nationalist, now deceased--might well be uncomfortable with some aspects of the presentation here.

Some Background:

As you (hopefully) know, history writing is not a simple matter of plotting a narrative of "what really happened" in the past. It is a much more complex act of construction and interpretation, often with profound political implications. The political issues of the day, as well as more subtle cultural biases and orientations, inevitably influence the writing of history. Politics in modern Japan from the late nineteenth century until 1946 especially, and to some extent continuing to the present day, have been carried out within the context of what is often called "The Emperor System" (tennōsei 天皇制). The role of the emperor in modern Japanese politics is a complex issue that we take up in HIST 481 in detail. Very briefly, however, the men who overthrew the Tokugawa Bakufu in 1867-8 and established a new, centralized state, did so in the name of the Meiji Emperor (thus ushering in the Meiji Period, 1868-1912).

Even during the early decades of the Meiji period, historical debates dealing with matters that might cast a shadow on the legitimacy of the reigning emperor were highly sensitive subjects. In 1882, for example, controversy erupted over an article by Shigeno Yasutsugu 重野安繹 (1827-1910) of the government's Bureau of Historical Writing (shūshikyoku 修史局), which later became the history department of Tokyo Imperial University. Shigeno's article attacked the account of the Northern and Southern Courts appearing in the prestigious Dai Nihon shi (大日本史 Great history of Japan) According to Susan Burns:

Shigeno argued that the the Dai Nihon shi relied uncritically on the description of events that appeared in the fourteenth-century chronicle Taiheiki, which he characterized as an unreliable source. The article, which cast doubt upon the legitimacy of the imperial line of which the Meiji emperor was the end product, led to a storm of criticism and earned Shigeno the nickname of "the erasing professor" (massatsu kyōju [抹殺教授]) because of the perception that he wanted to reject long-established "facts." [His opponents] responded by publishing a stream of articles in which they attacked Shigeno's "subversionism." (Susan Burns, Before the Nation: Kokugaku and the Imagining of Community in Early Modern Japan [Durham, NC: Duke University Press, 2003], p. 193.)

In 1882, the criticism of Shigeno, while severe and often ideologically motivated, remained largely an academic matter and did not seriously impede his career. The times, however, were changing. Just a decade later, another prominent historian who wrote an article that offended many imperial ideologues was forced by the government to resign his university position.

As time when on, politicians increasingly utilized the emperor as an ideological tool to enhance their power, both vis-à-vis political opponents and vis-à-vis the general population. By the 1930s (if not earlier), the emperor had become, for all intents and purposes, a national fetish object. Indeed, after 1936 it became illegal for ordinary citizens even to gaze upon the emperor. One key tenet of the ideology accompanying this fetishization of the emperor was that Japan's line of emperors has existed as a unified, unbroken line of descent for thousands of years, unlike the dynasties of other places such as China, which typically lasted but 2-3 centuries. This allegedly unbroken, unified line of emperors, reaching back into the misty recesses of antiquity, formed the basis of Japan's "national essence," which was summed up in the term kokutai 国体.

This obsessive focus on an alleged unified, unbroken line of emperors as the foundation of a special Japanese national essence presented a practical problem in the realm of history education. The basic problem was that the history of Japan's emperor was in fact quite complex and messy, full of division and conflict. Although there were several points in the narrative of Japan's history at which history teachers in the 1930s had to tiptoe with great care, the period of the opposition between the Northern and Southern Courts (officially, 1335-1391) was most problematic. Not only was it bad enough that two branches of the imperial family were at war with each other, but modern ideologues unanimously agreed that the Southern branch was legitimate. Problematically, however, the current reigning emperor (in the 1930s it was Hirohito, the Shōwa Emperor) was a descendant of the Northern branch. To provide a concrete sense of the problematic nature of the Northern and Southern Courts in modern Japanese history, I have translated most of a detailed lesson plan for elementary school teachers as it appeared in a Ministry of Education guide for history teachers published in 1937.

After 1946, the intensity of the fetishization of the emperor rapidly diminished as a result of Japan's defeat in the Pacific War. The emperor's official status became that of a constitutional monarch similar to the British monarchy, a fully-human symbol of the nation with no significant political power. The long legacy of the Japan's emperor system, however, continued to cast a shadow over national political life to at least some extent. There is a small but vocal (and sometimes violent) right-wing fringe that seeks to restore the emperor to his former pre-war glory. Though in no danger of swaying public opinion, these fanatics are quite willing to tray and assassinate any major political figure who, in their eyes, casts aspersions on the emperor. A famous recent case involved the mayor of Nagasaki, Motoshima Hitoshi, who in 1988 stated publicly that Emperor Hirohito bore some responsibility for the devastation of the Pacific War, in response to a question about this matter during a routine news conference. His comments cause a sensation throughout Japan, and the mayor was placed under round-the-clock guard. Nevertheless, after the security slackened, an assassin's bullet found its mark, seriously wounding the mayor in 1990. Mayor Motoshima survived the attack and even went on narrowly to win re-election. The key point here is simply  to see that issues surrounding the emperor remain potentially explosive in today's Japan.

In postwar Japan (1946 onward), history education became much less fraught with political danger and much more a tedious task of memorizing vast quantities of factual information. Still, the Ministry of Education approves all textbooks, and matters concerning the emperor remain sensitive. With this brief background in mind, let us now continue the story of the Northern and Southern Courts.

The Rest of the Story:

Consider this question: What constitutes imperial legitimacy in a case like the Northern and Southern Courts? If the key factor was political power, such as control of the capital or control of a majority of the country's territory and support of the majority of the country's warlords, then it is the Northern Court that steadily grew dominant from the 1340s onward. But as you noticed if you read the translated lesson plan mentioned previously, the key issue was possession of the imperial regalia (an ancient sword, mirror, and set of jewels). As Japan's emperor became a national fetish, these regalia took on the quality of fetish objects as well. From the standpoint of 1937, possession of these objects was the sole legitimating factor. Therefore, the Southern Court, which possessed the objects until 1391, was legitimate until the moment it delivered them to the Northern Court, which then--and only then--became the legitimate imperial court. Even today, although the emphasis is greatly toned down, textbooks portray possession of the regalia as the decisive factor in legitimacy, and the story ends in 1392 when the Southern Court concluded a peace treaty with the Northern Court and transferred the sacred objects.

What the textbooks do not say, however, is that this peace treaty was but a brief interlude in a conflict that continued much longer. One condition of the peace treaty was that Go-Kameyama (of the Southern branch) would recognize Go-Komatsu (the Northern emperor), but that Go-Kameyama’s son would succeed Go-Komatsu and that the Northern and Southern  lines of the imperial family would alternate taking the throne, as had been the case before Go-Daigo. When Go-Komatsu broke this agreement, setting up his own son as crown prince, Go-Kameyama secretly left Kyoto and returned to Yoshino. The Ashikaga shōgun was taken by surprise, dismayed to see the re-emergence of the southern court (Go-Kameyama plus local military supporters in the Yoshino area such as the Kusunoki, Ochi, and Miwa clans). This second court lasted 70 years as was called the Go-Nanchō 後南朝, or "Second Southern Court." In short, despite what the textbooks say, the conflict between the two branches of the imperial family did not end in 1391.

Some might object that this second court was only a local power without nation-wide influence, but there is another problem not so easily dismissed: the so-called Kakitsu no hen 嘉吉の変 (Kakitsu Incident) of 1443,  in which a Southern Court grandson of former Emperor Go-Murakami invaded Kyoto, forced his way into the Seiryōden Palace, seized the Imperial jewels (only, the sword and mirror were elsewhere and remained in Kyoto), and brought them back to Yoshino. So if possession of the regalia is the proper standard, then what about the status of Go-Hanazono, the reigning emperor at the time? One suspects that for modern textbook writers the matter is best left unmentioned. It was not until 1457 that an assassin killed Ichinomiya Jitennō 一宮自天王, the Southern Court “emperor,” and returned the jewels to Kyoto. But the second Yoshino court did not vanish even at this point.

Ten years later, in 1467, the Ōnin War devastated Kyōto. One warlord, Hosokawa Katsumoto 細川勝元 established his camp in the east and supported Emperor Go-Tsuchimikado 後土御門. His opponent, Yamana Sōzen 山名宗全, set up a western camp and supported the Second Southern Court “emperor” Oguranomiya 小倉宮. So it is perfectly reasonable to see the Ōnin War as an extension of the earlier war between the Northern and Southern Courts. Therefore, the opposition between the two courts dragged on for over 130 years, not the 56 years given in textbook accounts—longer even than the 100 Years’ War in Europe.

And the story does not end in 1467. After approximately 1470, the Yoshino area gradually calmed down for various reasons, but the Southern Court supporters still refused to acknowledge the legitimacy of Kyoto. They continued to bear a grudge and prepare for possible military action throughout the rest of the Muromachi period and even throughout the Tokugawa period. In 1863, there was the Tenchūgumi no Ran (天誅組の乱 or 天忠組の乱), also known as the Yamato Gikyo 大和義挙, in which Yoshino-based leaders raised an army in an effort to topple the Tokugawa bakufu. It is as if the Yoshino court supporters had been existing in dormant or potential state until that point and then suddenly materialized. Even today, some 200 households perform rites in memory of their Yoshino court ancestors at the time of the old lunar new year.

Interestingly, during the early months of the U.S. occupation of Japan in late 1945, numerous relatively ordinary people from around Japan made claims to being the rightful heirs to Japan's imperial throne, which they backed up with genealogical data. John W. Dower makes the following observation about this matter:

The most intriguing claimant to the chrysanthemum throne first brought his case to GHQ [General Headquarters] in September 1945 and saw it emerge as a topic of public interest in January. He was a fifty-six-year-old variety-store proprietor from Nagano named Kumazawa Hiromichi, who attracted particular interest because his claim rested on a genuine genealogical dispute tracing back to the fourteenth century, when the imperial line had split into fiercely contentious "northern" and "southern" courts. Hirohito belonged to the northern line, but there were serious grounds for arguing that the southern line--from which Kumazawa claimed descent--was the more legitimate and should have carried on the imperial tradition.

. . . Among other things, Kumazawa's claim cast serious doubt on the vaunted ideology of bansei ikki ("ten thousand generations in a single line") by which the modern imperial institution claimed unbroken descent from time immemorial. (Embracing Defeat: Japan in the Wake of World War II [New York: W. W. Norton & Company, 1999], pp. 306-307.)

Notice that, contrary the emphasis in official modern ideology on the emperor as a unifying force in Japan, the imperial family was frequently a divisive force. Owing to the official modern view, prewar textbooks in Japan sought to skip over the matter of the divided imperial court as fast as possible, blaming this apparent aberration on the evil Ashikaga Shōguns. Even contemporary textbooks (and the Ministry of Education bureaucrats who approve them) are unwilling to delve too deeply into the complexities of imperial-family-related conflict in Japan's history. The nearly 60-year period of the officially-recognized conflict between the two courts complicates maters enough. Why muddy the waters even further by telling the rest of the story? Leaving out complicating facts and details is a common rhetorical strategy in history writing and other forms of argumentation. Are you aware of any other such cases?