Genetic differentiation within a species’ range is determined by natural selection, genetic drift, and gene flow. Selection and drift enhance genetic differences if populations are sufficiently isolated, while gene flow precludes differentiation and local adaptation. Over large geographical areas, these processes can create a variety of scenarios, ranging from admixture to a high degree of population differentiation. Genetic differences among populations may signal functional differences within a species’ range, potentially leading to population or ecotype-specific responses to global change. We investigated differentiation within the geographical range of two butterfly species along a broad latitudinal gradient. This gradient is the primary axis of climatic variation, and many ecologists expect populations at the poleward edge of this gradient to expand under climate change. Our study species inhabit a shared ecosystem and differ in body size and resource specialization; both also find their poleward range limit on an island. We find evidence for divergence of peripheral populations from the core in both taxa, suggesting the potential for genetic distinctiveness at the leading edge of climate change. We also find differences between the species in the extent of peripheral differentiation with the smaller and more specialized species showing greater population divergence (microsatellites and mtDNA) and reduced gene flow (mtDNA). Finally, gene flow estimates in both species differed strongly between two marker types. These findings suggest caution in assuming that populations are invariant across latitude and thus will respond as a single ecotype to climatic change.