The capercaillie (Tetrao urogallus) is one of Poland's most endangered bird species, with an estimated population of 380-500 individuals in four isolated areas. To study these natural populations in Poland further, more than 900 non-invasive genetic samples were collected, along with samples from 59 birds representing large, continuous populations in Sweden and Russia; and from two centres in Poland breeding capercaillie. Microsatellite polymorphism at nine loci was then analysed to estimate within-population genetic diversity and genetic differentiation among populations. The results confirmed that isolation of populations and recent decreases in their sizes have reduced genetic diversity among capercaillie in Poland, with all the country's natural populations found to be experiencing the genetic after-effects of demographic bottlenecks. The results of analyses of genetic differentiation and structure further suggest the presence of a 'lowland' cluster (encompassing birds of the Augustowska and Solska Primaeval Forests in Poland, and of Sweden and Russia), and a Carpathian cluster. Capercaillie from Sweden and Russia are also found to differ markedly. The Polish lowland populations seem more closely related to birds from Scandinavia. Our genetic analysis also indicates that the stocks at breeding centres are of a high genetic diversity effectively reflecting the origins of founder individuals, though identification of ancestry requires further study in the case of some birds. Overall, the results sustain the conclusion that the Polish populations of capercaillie from the Carpathians and the lowlands should be treated as independent Management Units (MUs). This is to say that the breeding lines associated with these two sources should be maintained separately at breeding centres. The high level of genetic differentiation of birds from the Solska Primaeval Forest suggests that this population should also be assigned the status of independent MU.