Visiting a natural history or science museum is a secular pilgrimage: a duty of citizens of the modern world. How then should we interpret the Taishō era six-sided shrine that was erected in the commemoration building of the Nawa Insect Museum, with a sculptural image of Kannon placed within? Does the bodhisattva’s presence contradict the narrative of a modern scientific nation? What significance should we attribute to the fact that architect Takeda Goichi (1872-1938) reused wood pillars from the temple at Tōshōdai-ji to build the shrine and supports for the second floor of the museum building? The entomologist Nawa Yasushi (1857-1926) established the museum independently in 1919 with contributions from his local community. While art and architectural research on Japanese museums tends to focus on institutions supported at the national level, in this paper I go beyond the state-driven modernizing narrative to investigate initiatives of Meiji and Taishō era non-state actors. The museum is of special interest in that it engages directly with issues of Japanese national identity formation in the early twentieth-century. In contrast to the National Science Museum, which opened in 1931, I argue that Nawa’s institution operated in a kind of liminal modernity, accepting the comingling of past and future as an acceptable present. It did not exhibit a modern scientific identity solely based on scientific typologies of the time. Instead, Nawa and Takeda integrated existing and new symbolism at a time when Japanese “tradition” and “modernity” were often deemed to be at odds.