Understanding the impact of natural and anthropogenic landscape features on population connectivity is a major goal in evolutionary ecology and conservation. Discovery of dispersal barriers is important for predicting population responses to landscape and environmental changes, particularly for populations at geographic range margins. We used a landscape genetics approach to quantify the effects of landscape features on gene flow and connectivity of boreal toad (Bufo boreas) populations from two distinct landscapes in south-east Alaska (Admiralty Island, ANM, and the Chilkat River Valley, CRV). We used two common methodologies for calculating resistance distances in landscape genetics studies (resistance based on least-cost paths and circuit theory). We found a strong effect of saltwater on genetic distance of CRV populations, but no landscape effects were found for the ANM populations. Our discordant results show the importance of examining multiple landscapes that differ in the variability of their features, to maximize detectability of underlying processes and allow results to be broadly applicable across regions. Saltwater serves as a physiological barrier to boreal toad gene flow and affects populations on a small geographic scale, yet there appear to be few other barriers to toad dispersal in this intact northern region.