This article reconsiders the history of the reception of Comenius’ works in Japan. Whilst no event prior to the translation of Orbis pictus by the drifted fisherman Gonza in the first half of the 18th century was found through the examination of the catalogues of the books which flowed into Japan before the modern era, the works written by Comenius’ friend Johannes Jonston and his adversary Lodewijk Meyer played a considerable role in the development of the Western learning in Japan. Moreover, contrary to the fact that Comenius’ works were not unearthed, Japanese pictorial  textbook Kimmō zui compiled by the Confucian scholar Tekisai Nakamura reached Europe in the 17th century despite the feudal isolation policy. The taxonomy of the trilingual European vocabulary Sango benran compiled in Japan in the middle of the 19th century was influenced by European similar vocabularies, for which Comenius supposedly provided a philosophical base with the idea of “the Three Books of God”. Comenian taxonomy might have not been unfamiliar to Japanese intellectuals accustomed to that of Confucians based on the principle of “the Three Talents”.