<p>Habitat loss restricts movement between habitats, reducing genetic diversity and increasing wildlife’s vulnerability to environmental change. Landscape genetics can help identify how habitat loss and heterogeneity influence genetic diversity and genetic differentiation. For long-lived species such as turtles, long generation times can obscure declines in genetic diversity. Thus, it is important to consider how historic, or “ghost” landscapes influence genetic diversity. This study compared the impact of ghost and current habitat amount, configuration, and latitude on the genetic diversity of the Snapping Turtle (<i>Chelydra serpentina</i>), the Blanding’s Turtle (<i>Emydoidea blandingii</i>) and the Spotted Turtle (<i>Clemmys guttata</i>). We leverage genetic data from previous studies that have investigated population structure and provide a comparative synthesis on how landscape change is affecting these sympatric species. Allelic richness is lowest at sites with greater wetland loss exclusively in Snapping Turtles. While latitude showed no effect on genetic diversity across species, isolation by distance was significant. Drivers of genetic differentiation varied by species: Snapping Turtle was influenced by forest cover, Spotted Turtle by historic wetland loss, and Blanding’s Turtle by geographic distance. Isolation among species due to landscape change and reduced genetic diversity in Snapping Turtles suggest vulnerability to continued habitat loss. This synthesis using data from previous studies provides novel inference and conservation value due to the previously unexamined impact of landscape heterogeneity and latitude on sympatric species nearing their northern range limit. These findings highlight varied responses to habitat loss and the need for habitat restoration that addresses multiple species’ conservation needs.</p>