Most institutional theories of the diversity of capitalism (at least implicitly) assume the existence of a representative firm in each type of capitalism. Based on a case study of Japan during the Lost Decade (1992–2005), this paper aims at showing that this assumption introduces severe drawbacks in the analysis of Japanese capitalism in crisis. After having proposed a survey of theories of Japanese capitalism and of its crisis, we assess the increasing heterogeneity of Japanese firms since the beginning of the 1990s, in terms of performances and “models”, and propose some explanations of this increasing heterogeneity, which concerns firms of similar size and belonging to the same sectors. We then propose an alternative interpretation of this crisis — the lack of coordination of an increasing heterogeneity — and argue that it requires a new characterization of Japanese capitalism. In the final part, we extend our analysis beyond the Japanese case in arguing that our framework, which is based on an alternative theory of the firm, on the study of the evolution of the heterogeneity of organizations, and on the analysis of aggregation and coordination of the micro behaviors through institutions, provides a more dynamic understanding of institutional change.