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Anthropogenic factors such as land-use change, pollution, and climate change can cause fragmentation and reduce the amount of habitat by altering preferred conditions. This process can also bring about novel species interactions and, in some cases, create or alter levels of hybridisation between closely related species. We assessed the threat of hybridisation to the persistence of the Rocky Mountain sculpin (Cottus sp.) and the slimy sculpin (Cottus cognatus) in the Flathead River, British Columbia, Canada. Individuals collected from 95 sites provided 731 genetic samples that were genotyped at 10 polymorphic microsatellite loci and mitochondrial cytochrome C oxidase sequences, to assess: (a) if there are differences in the distribution of Rocky Mountain sculpin between contemporary and historical (35 years ago) records, (b) if hybridisation is symmetrical in terms of sex-specific parental contributions, and (c) if habitat preferences contribute to the distribution of pure parental and hybrid populations. We identified three hybrid locations and that Rocky Mountain sculpin have an altitudinal distribution (1,200-1,902 m) that exceeds the range limit reported 35 years ago (1,200-1,372 m). Additionally, hybrid mating appears to involve similar proportions of parents of both sexes from each species. Lastly, elevation, turbidity, and sediment type are significant factors predicting the presence of parental species. Further, elevation and water conductivity are significant factors to predicting hybrid presence. The contrasting associations of parental species with different habitat types appear to influence the extent and distribution of hybridisation. Our results suggest that Rocky Mountain sculpin (a species of conservation concern) do not appear to be at risk due to hybridisation, but that this is a system in flux. Given the importance of environmental conditions to hybridisation, there is a need to quantify how environmental changes may disrupt current hybridisation and potential population viability.