Patterns of genetic and phenotypic variation within and among populations are influenced by a complex interplay of ecological and evolutionary processes. Theory posits that gene flow should increase diversity within and reduce differentiation between populations. Evaluating these predictions is potentially complicated by selection, population dynamics and plasticity that may also affect genetic and phenotypic variation. Here, we compare genetic and morphological variation between sympatric populations of two pygmy grasshopper species, Tetrix subulata and T. undulata, that differ in dispersal capacity. We found that genetic differentiation between populations is lower on average in the generally dispersive T. subulata compared with the mostly sedentary T. undulata, suggesting that genetic structure in the latter species has been less influenced by the homogenizing effects of migration. Our results also provided weak support for the hypothesis that neutral genetic diversity within populations should be higher in T. subulata than in T. undulata. We further found that body size varied among populations in both species, but the differences seen in T. subulata did not parallel those seen in T. undulata, indicating that the two species have unique plasticity responses or that they have responded differently to shared selective regimes. Our findings illustrate the utility of the pairwise comparative approach and further highlight that results and conclusions may not be transferrable even between closely related species.