The importance of assessing spatial layers at multiple spatial-scales when modeling species environmental relationships has been highlighted by several empirical studies. However, no landscape genetics studies have optimized landscape resistance surfaces by evaluating relevant spatial predictors at multiple spatial-scales. Here, we model multi-scale/layer landscape resistance surfaces to estimate resistance to inferred gene flow for two vernal pool breeding salamander species, spotted (A. maculatum) and marbled (A. opacum) salamanders. Multi-scale resistance surface models outperformed spatial layers modeled at their original spatial scale. A resistance surface with forest land cover at a 500m Gaussian kernel bandwith, and normalized vegetation index at a 100m Gaussian kernel bandwidth was the top optimized resistance surface for A. maculatum. A resistance surface with traffic rate and topographic curvature, both at a 500m Gaussian kernel bandwidth was the top optimized resistance surface for A. opacum. Species-specific resistant kernels were fit at all vernal pools in our study area with the optimized multi-scale/layer resistance surface controlling kernel spread. Vernal pools were then evaluated and scored based on surrounding upland habitat (local score) and connectivity with other vernal pools on the landscape, with resistant kernels driving vernal pool connectivity scores. As expected, vernal pools that scored highest were in areas within forested habitats and with high vernal pool densities and low species-specific landscape resistance. Our findings highlight the success of using a novel analytical approach in a multi-scale framework with applications beyond vernal pool amphibian conservation.