Separating historical effects from recent anthropogenic pressures on population structure is paramount for understanding how species have persisted over time and how conservation efforts should best proceed. In this issue of Molecular Ecology, Chiucchi & Gibbs (2010) have separated the impacts of ancient and modern habitat fragmentation on genetic structure and migration rates in an endangered species of rattlesnake, the eastern massasauga (Sistrurus catenatus). Previous studies have ignored ancient processes, estimated genetic isolation and migration using collections from different timescales, used markers with different rates of evolution or compared contemporary populations in both continuous and fragmented habitats (Keyghobadi 2007). Here, Chiucchi & Gibbs (2010) estimate migration parameters from microsatellites at two timescales using coalescent methods. Results strongly suggest that massasaugas are characterized by the low levels of migration with strong regional and range-wide differences, typical of many organisms residing in the patches of habitat surrounded by seas of agriculture, but that these patterns have existed since the Pleistocene. The novel methodology and hypotheses addressed in Chiucchi & Gibbs (2010) highlight future avenues for examining the impacts of fragmentation through time.