Due to its critical location on the Nile River controlling trade from the south, Tombos is an important ancient site to explore the interaction between Egyptians and Nubians. To assess population continuity at Tombos through sociopolitical transitions, the appendicular skeleton of people from the New Kingdom and Napatan periods was examined. Using morphometric and statistical analyses, body proportions on the upper and lower limbs were studied on each element through size (i.e. length, breadth, and width) and shape (bone's measurements with size removed). The Napatan component (when Nubia ruled Egypt) was consistently larger in size than the earlier New Kingdom component (when Egypt ruled Nubia), with little variation in shape. More variability in both size and shape was observed in males. When compared with other Nubians (C‐group and Kerma) and Egyptians (Middle and New Kingdom), the Tombos Napatan sample (males and females) was generally larger, whereas the Tombos New Kingdom sample was generally smaller than other Nubians and similar in size to Egyptians. Some of the variability between the Tombos samples may be the result of gene flow, or rather changes in migration to the area through time and sociopolitics. However, the numerous differences in size with few in shape provide more support for an environmental explanation since size is more susceptible to nutritional stress, disease, and physical activity. These results show that the people of Tombos underwent biological alterations during these major sociopolitical changes from Egyptian rule over Nubia during the New Kingdom to Nubia ruling Egypt during the Napatan period. This study also demonstrates that morphometric analyses of multiple bones and measurements are an important supplement to other bioarchaeological analyses to provide a broader of view of physical changes that occur over time. Copyright © 2014 John Wiley & Sons, Ltd.