Species ranges which span different geographic landscapes frequently contain cryptic species or population-level structure. Identifying these possible diversification factors can often be accomplished under a comparative phylogeographic framework. However comparisons suffer if previous studies are limited to a particular group or habitat type. In California, a complex landscape has led to several phylogeographic breaks, primarily in terrestrial species. However two sister taxa of freshwater fish, riffle sculpin (Cottus gulosus) and Pit sculpin (C. pitensis), display ranges based on morphological identifications which do not coincide with these breaks. Using a comprehensive sampling and nuclear, mitochondrial, and microsatellite markers, we hypothesized proposed species ranges are erroneous based on potential hybridization/gene flow between species. Results identified a phylogeographic signature consistent with this hypothesis, with breaks at the Coast Range Mountains and Sacramento/San Joaquin River confluence. Coastal locations of C. gulosus represent a unique lineage and “true” C. gulosus were limited to the San Joaquin basin, both regions under strong anthropogenic influence and potential conservation targets. C. pitensis limits extended historically throughout the Sacramento/Pit River basin but currently are restricted to the Pit River. Interestingly, locations in the Sacramento River contained low levels of ancestral hybridization and gene flow from C. gulosus but now appear to be a distinct population. The remaining population structure was strongly correlated with Sierra Nevada presence (high) or absence (low). This study stresses the importance of testing phylogeographic breaks across multiple taxa/habitats before conservation decisions are made, but also the potential impact of different geographic landscapes on evolutionary diversification.