Life exhibitions in Japanese science museums (SMs) face difficulties in coping with rapid progress in the life sciences owing to certain constraints around the frequency of exhibit renovations, and the Japanese indigenous understanding of the natural world (Shizen) that Japanese visitors unconsciously bring with them. To what extent do current life exhibitions reflect aspects of Japanese Shizen as well as recent progress in the life sciences? The purpose of this study was twofold: to analyse the contents of life exhibitions in nine Japanese SMs from both a Japanese Shizen and a contemporary life science perspective. The major findings were: (1) educational missions in natural history institutions appreciated and reflected Japanese indigenous understanding of Shizen in addition to having a scientific understanding of life phenomena; (2) from a life science perspective, among the "common traits of life," "evolution" was the most commonly exhibited trait, while "genome" was the least; and (3) the importance of DNA and genomes in contemporary life sciences was not yet fully appreciated in most of the institutions. The findings implied that in natural history institutions life exhibitions could emerge as a kind of amalgam of Shizen and life science to the visitors. The need for a careful means to avoid the potential misunderstanding of life sciences by visitors is discussed.