We have an ongoing genetic monitoring program in Central Idaho’s Salmon River Basin to evaluate population genetic structure and potential changes in diversity of Oncorhynchus mykiss populations through time. Our results show distinct populations both within and among the major Salmon River tributaries, consistent with isolation by distance. However, an exception to this pattern was found between two headwater populations in different river basins: Marsh Creek in the Middle Fork Salmon River was genetically similar to Valley Creek in the main stem Salmon River. The waterway distance between these sites is over 500 km but the geographic distance is only about 200 m across a marshy, meadow-like, blind summit. Both population-level genetic analyses and model-based clustering suggest recent gene flow. Apparently, this area is subjected to periodic local flooding during spring snowmelt that allows intermittent access to Marsh Creek by Valley Creek fish. In this study, we describe specific patterns of isolation by distance with the exception highlighted. Our results are relevant to conservation and recovery of Salmon River steelhead as well as the broader understanding of population genetics and phylogeography of salmon and steelhead throughout the Pacific Northwest.