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Identifying drivers of dispersal limitation and genetic differentiation is a key goal in biogeography. We examine patterns of population connectivity and genetic diversity using restriction site‐associatedDNAsequencing (RADseq) in two bumble bee species,Bombus vosnesenskiiandBombus bifarius,across latitude and altitude in mountain ranges from California, Oregon and Washington, U.S.A.Bombus vosnesenskii, which occurs across a broader elevational range at most latitudes, exhibits little population structure whileB. bifarius, which occupies a relatively narrow higher elevation niche across most latitudes, exhibits much stronger population differentiation, although gene flow in both species is best explained by isolation with environmental niche resistance. A relationship between elevational habitat breadth and genetic diversity is also apparent, withB. vosnesenskiiexhibiting relatively consistent levels of genetic diversity across its range, whileB. bifariushas reduced genetic diversity at low latitudes, where it is restricted to high‐elevation habitat. The results of this study highlight the importance of the intersect between elevational range and habitat suitability in influencing population connectivity and suggest that future climate warming will have a fragmenting effect even on populations that are presently well connected, as they track their thermal niches upward in montane systems.