Diversity of human body size and shape is often biogeographically interpreted in association with climatic conditions. According to Bergmann's and Allen's rules, populations in regions with a cold climate are expected to display an overall larger body and smaller/shorter extremities than those in warm/hot environments. In the present study, the skeletal limb size and proportions of prehistoric Jomon hunter-gatherers, who extensively inhabited subarctic to subtropical areas in the ancient Japanese archipelago, were examined to evaluate whether or not the inter-regional differences follow such ecogeographic patterns. Results showed that the Jomon intralimb proportions including relative distal limb lengths did not differ significantly among five regions from northern Hokkaido to the southern Okinawa Islands. This suggests a limited co-variability of the intralimb proportions with climate, particularly within genealogically close populations. In contrast, femoral head breadth (associated with body mass) and skeletal limb lengths were found to be significantly and positively correlated with latitude, suggesting a north-south geographical cline in the body size. This gradient therefore comprehensively conforms to Bergmann's rule, and may stem from multiple potential factors such as phylogenetic constraints, microevolutionary adaptation to climatic/geographic conditions during the Jomon period, and nutritional and physiological response during ontogeny. Specifically, the remarkably small-bodied Jomon in the Okinawa Islands can also be explained as an adjustment to subtropical and insular environments. Thus, the findings obtained in this study indicate that Jomon people, while maintaining fundamental intralimb proportions, displayed body size variation in concert with ambient surroundings. Am J Phys Anthropol, 2012. © 2012 Wiley Periodicals, Inc.