Objective The Jomon, one of the ancestral populations of modern Japanese, were hunter‐gatherers inhabiting the Japanese archipelago from 11,000 to 300 BC. We evaluated changes in the diaphyseal morphology of the fibula from the middle to the final phase of the Jomon period, compared to the morphology of other historical and modern populations from the Japanese archipelago, to elucidate temporal changes in habitual activities and possible division of labor among males and females. Material and Method Jomon specimens of 107 males and 97 females were obtained from the shell mounds of the Pacific coastal area of East Japan, distinguishing between middle (3,000–2,000 BC) and late‐final (2,000–300 BC) phases of the Jomon period. Mid‐shaft morphology of the fibula and tibia were compared to morphological measurements of specimens from Yayoi (37 males, 28 females), medieval (56 males, 56 females), early modern (51 males, 50 females), and modern (125 males, 68 females) periods. Result Largest values of fibular areas and relative fibular‐to‐tibial areas were identified in males from the late‐final Jomon phase, compared to the middle Jomon phase and after the Yayoi period. These period‐specific differences in fibular area were smaller in females, with the largest between‐sex difference identified in the late‐final Jomon phase. Discussion Results confirm a change in the habitual activity pattern of males in the late‐final phase. Males of the late‐final Jomon phase likely did more long‐distance traveling to the inland/mountainous region, as part of an ecological change that occurred during the middle to the late‐final Jomon phase. Am J Phys Anthropol 160:708–718, 2016. © 2016 Wiley Periodicals, Inc.