In this study, we examine the effects of habitat fragmentation on the genetic structure of the Cantabrian capercaillie Tetrao urogallus cantabricus, based on eight microsatellite loci in non‐invasive samples collected across its entire distribution range in northern Spain. For this purpose, we used Bayesian clustering methods and landscape connectivity analyses. We found low genetic diversity and significant genetic differentiation across the subspecies distribution range. Based on the isolation‐by‐distance pattern observed, we hypothesized that the low dispersal of the species and the habitat configuration might be shaping the genetic structure of Cantabrian capercaillie, and cause reduced gene flow and diversity of some areas. Three genetic clusters were inferred, one in the northern and two in the southern slope of the Cantabrian Mountains. Our results suggest that small but abundant forest patches on the northern slope of the Cantabrian range do not seem to represent a barrier to gene flow, whereas the more isolated forests in the southern Cantabrian Mountains do represent such a barrier. This result was not concordant with the structure proposed based on lek occupation patterns. Conservation strategies should include restoration of forest connectivity to the extent possible.