Human-induced changes in the natural environment impact upon a wide variety of genetic processes at all levels of population structure. Insight into these processes is now achieved by analyses of genetic diversity allowing the past and present condition of populations to be assessed and compared. Given its severe fragmentation and small size, the population of the Capercaillie Tetrao urogallus in Poland can be regarded as especially prone to gene-pool alteration. Moreover, this is a region of Europe in which different genetic lineages of the Capercaillie may be present, ensuring that certain conservation decisions may be even more difficult than they otherwise would be. Bearing the above in mind, we decided to study polymorphism of the mitochondrial DNA Control Region (mtDNA CR) in remnant and extinct populations of the Capercaillie in Poland. The extinct population was represented by samples from birds hunted in the Lower Silesian Forest (SW Poland) between 1951–1962. We compared sequences obtained with data from the large, continuous population present in Russia and Scandinavia. Analysing 331 bp of mtDNA CR for 168 individuals, we identified 24 haplotypes, among which only 6 had not been reported previously in the species according to GenBank. Our data confirmed a previous suggestion regarding the genetic structure of the species in Poland, i.e. that birds from Augustów Forest (NE Poland) are related to Russian and Scandinavian populations, constituting a part of the lowland group within the boreal lineage. The Carpathian population is in turn confirmed as an independent genetic group within the boreal lineage, while specimens from the Solska Forest (SE Poland) prove to be highly differentiated from birds in other Polish populations; most likely because they derive from — or have been connected via gene flow with — birds present in the Balkans. Further genetic analysis is necessary to resolve this evolutionary relationship between Capercaillies from south-eastern Poland and those of the Balkans. Where practice is concerned, the overall advice is that three Conservation Units are to be recognised in Poland. In addition to those, the extinct population from the Lower Silesian Forest has been deemed part of the lowland group within the boreal lineage, albeit a distinctive one, given the possibility of gene exchange with Carpathian birds. We further suggest that some aspect of this extinct population's genetic diversity reflects an uncontrolled process of reintroduction taking place in the past.