["International Journal of Osteoarchaeology, Volume 36, Issue 2, Page 260-270, March/April 2026. ", "\nABSTRACT\nEndocranial morphology may serve as a relatively neutral trait shaped by genetic drift. This study aimed to clarify genetic and population history in the Japanese Archipelago by comparing three‐dimensional endocast shape among Jomon (c. 16,000–2300 bp), Yayoi (c. 2300–1700 bp), and modern Japanese. CT data from 105 crania (39 Jomon, 10 Yayoi, 56 modern Japanese) were used to reconstruct endocasts. A total of 171 landmarks and semilandmarks were acquired, including estimated points for incomplete specimens. Generalized Procrustes analysis and principal component analysis (PCA) were applied to assess shape variation, and intergroup differences were tested. Jomon endocasts were characterized by posterior elongation, frontal depression, and wider posterior cranial fossae, separating them from Yayoi and modern Japanese. Yayoi endocasts displayed significantly greater anterior cranial base width and distinctive shape features compared with both Jomon and modern Japanese. Importantly, Jomon from western Japan differed significantly from those in central‐eastern Japan, indicating regional variation within Jomon populations. The overlap of Yayoi with modern Japanese along PC1 supports their closer affinity, while distinctive Yayoi traits emerged in other PCs. The marked difference between Jomon groups suggests more regional diversity than previously recognized. Overall, endocranial shape provides an informative, largely neutral marker of genetic relationships, potentially complementing genomic and skeletal evidence. This study offers new insights into the formation and diversification of Japanese populations.\n"]