Knowledge about changes occurring in the genetic structure of populations is extremely important in the case of endangered species. Research studies conducted in space and time allow us to identify factors that are influencing gene flow. Especially in the case of species occurring in the form of dispersed, more or less isolated populations, this is crucial for developing effective conservation strategies. The Carpathians are one of the most important capercaillies stronghold in Central Europe. The population here is fragmented, and at least, some groups of birds are small and isolated. This study aimed to determine whether the genetic structure of the capercaillie in the Polish part of the Carpathians has changed over the last decade. The research was conducted in three Polish national parks: Babia Góra National Park (BAB), Gorce (GOR) and Tatra (TAT). A total of over 1,300 non-invasive samples were collected for genetic analyses in two periods: 2010–2013 and 2021–2022. Individuals were identified using microsatellite markers. It was found that during the research period, there were approximately 200 capercaillie individuals in the Parks. The level of genetic variability in individual strongholds has not changed significantly. However, traces of a new gene pool were found in BAB, which could have appeared from other areas of the Carpathians where the species is being reintroduced. GOR shows features of a sink population: low genetic variability, low number of individuals and gradual decline in emigration. During the period covered by the study, the genetic structure has changed little: the studied strongholds are partially genetically isolated, but gene flow between BAB and GOR appears to be increasingly limited. TAT is a hybrid and transition zone for gene flow between smaller strongholds. The results emphasize the importance of areas with stable, numerous populations for the survival of smaller, peripheral groups of the capercaillie in mountain areas.