question: Non-human primates are our closest relatives and therefore offer valuable comparative models for human evolutionary studies and biomedical research. As such, Japanese macaques (Macaca fuscata) have contributed to the advancement of primatology in both field and laboratory settings. Specifically, Japanese macaques serve as an excellent model for investigating postnatal development and seasonal breeding in primates because of their relatively prolonged juvenile period and distinct seasonal breeding activity in adulthood. Pioneering histological studies have examined the developmental associations between their reproductive states and spermatogenesis by morphological observation. However, a molecular histological atlas of Japanese macaque spermatogenesis is only in its infancy, limiting our understanding of spermatogenesis ontogeny related to their reproductive changes. Here, we performed immunofluorescence analyses of spermatogenesis in Japanese macaque testes to determine the expression of a subset of marker proteins. The present molecular histological analyses readily specified major spermatogonial subtypes as SALL4+ A spermatogonia and Ki67+/C-KIT+ B spermatogonia. The expression of DAZL, SCP1, γH2AX, VASA, and calmegin further showed sequential changes regarding the protein expression profile and chromosomal structures during spermatogenesis in a differentiation stage-specific manner. Accordingly, comparative analyses between subadults and adults identified spermatogenic deficits in differentiation and synchronization in subadult testes. Our findings provide a new diagnostic platform for dissecting spermatogenic status and reproduction in the Japanese macaques.