Porotic hyperostosis (PH) is the skeletal marker used in the estimation of physiological stress suffered in childhood. Despite a conventional hypothesis that mankind’s health conditions declined with the advent of agriculture, there are few reports comparing the PH seen on ancient crania of hunters-fishermen-gatherers and agrarian peoples. In this study, we examined the crania of 16th to 19th century Eurasian peoples: Siberian natives (hunters-fishermen-gatherers), Russian settlers, and Joseon Koreans (agriculturalists) to see whether PH could be observed to differ between populations with varying subsistence strategies. The prevalence of PH decreased in the order of Joseon people (18.9 %), Russian settlers (6.3 %), and Siberian natives (3.8 %). In brief, the hunters-fishermen-gatherers’ stress level was lower than agriculture-based Joseon people and Russian settlers. In addition, Joseon people might have been exposed to more serious stressful episodes than Russian settlers were. We assume that the former might have lived under much stressful conditions than the latter did, though both people depended on intense agriculture. As for sexual dimorphism of PH: in all groups, males were identified with more PH signs than females were. Our report successfully shows that the detailed pattern of stress markers might have been influenced by complex interactions between various factors that existed under different conditions in history.