Wildlife conservation and management of endangered species requires reliable information on the size and structure of populations. One of the flagship species in European wildlife conservation is the forest-dwelling capercaillie (Tetrao urogallus), where several populations are endangered. In the Bohemian Forest, e.g., the population severely declined 30 years ago with only 100 birds remaining in 1985. Subsequently, breeding and release programs were conducted to supplement the local population. The current distribution and population size, however, remained unknown. With recent habitat changes and increasing recreational activities, a reliable population estimate to inform conservation plans was needed. A team of scientists and volunteers collected fresh capercaillie droppings covering an area of about 120,000 ha. We genotyped ten microsatellite loci to estimate the current population size and to determine the population's spatial and genetic structure.Population size and density estimators revealed a population size of approximately 500 individuals, which is thus one of the two largest relict populations in the low mountain ranges of temperate Europe. The population clustering revealed gene flow across the entire study area. Several genotypes were documented with multiple recaptures at spatial distances between 10 and 30 km additionally corroborating gene flow across the entire landscape of the study area. Males were more closely related than females on small spatial scales up to 3 km, indicating lower dispersal rates in males. We conclude that the population currently appears to have a viable size and shows unrestricted gene flow across state borders and management units of the entire Bohemian Forest. However, long-term viability of this population requires a transboundary strategy to sustainably protect and monitor this isolated capercaillie population in Central Europe.