Understanding how selective forces influence patterns of symmetry remains an active area of research in evolutionary biology. One hypothesis, which has received relatively little attention, suggests that the functional importance of morphological characters may influence patterns of symmetry. Specifically, it posits that for structures that display bilateral symmetry, those with greater functional importance should display lower levels of asymmetry. The aim of this study was to examine the patterns of fluctuating asymmetry (FA) present in the limb bones of freshwater turtles in the family Emydidae. Aquatic emydid turtles of the subfamily Deirochelyinae employ a hindlimb‐dominant swimming style, suggesting that hindlimbs should display lower levels of FA. Consistent with the morpho‐functional hypothesis of symmetry, we found a strong, clade‐wise pattern of humeral‐biased FA in aquatic Deirochelyinae. In contrast, some emydids of the subfamily Emydinae possess more terrestrial tendencies. As terrestrial locomotion places more equal importance on fore‐ and hindlimbs, we predicted that such behaviors may minimize differences in FA. No clade‐wise pattern was detected in the subfamily Emydinae. We also detected a phylogenetic signal in FA within the femur and discovered that FA has evolved at vastly different rates between the fore‐ and hindlimbs.