Large terrestrial carnivores are particularly prone to factors constraining levels of population genetic diversity because of their low densities and high spatial requirements. We studied the pattern of Eurasian lynx Lynx lynx population genetic variability in the westernmost part of its natural range from Scandinavia to the Carpathian Mountains (north-central Europe) based on 190 samples using 613 base pair-long sequences from the mitochondrial DNA control region (mtDNA-cr). We examined whether the population history or contemporary habitat constraints of this large and mobile carnivore could have significantly affected its genetic structure. We recorded nine mtDNA haplotypes, including five not previously reported. Lynx from Latvia and Estonia had the highest variability with haplotype and nucleotide diversities of 0.81–0.88% and 0.44–0.47%, respectively. In contrast, there was no polymorphism present in peripheral populations from Norway and the Carpathian Mountains. Lynx populations were strongly differentiated [analysis of molecular variance (AMOVA): Φ ST = 0.570, P < 0.001, F ST = 0.464, P < 0.001)]. Spatial Analysis of Molecular Variance identified four separate groups of populations: (1) Norway, Finland and Estonia; (2) Latvia and North Eastern Poland; (3) the Białowieża Primeval Forest; (4) the Carpathians. The patterns of genetic diversity and differentiation suggested a number of discrete populations that are poorly connected by contemporary gene flow and could therefore be considered demographically independent. The peripheral location of these populations, habitat fragmentation and the strict territorial structure of lynx populations are factors likely contributing to the observed patterns. The study provides suggestions for active conservation/management decisions including translocations or reintroductions of lynx.