The effect of philopatry on the formation of the intrapopulation structure in the crested auklet colony of the Talan Island, Taui Bay of the Sea of Okhotsk, was examined. The nucleotide sequences of the mitochondrial DNA control region fragment (408 bp) and five microsatellite loci (Apy03, Apy04, Apy06, Apy07, Apy10) in individuals from two study plots of the colony were examined. A high genetic diversity (h = 0.999 ± 0.003) and the absence of intrapopulation genetic differentiation was observed at both types of markers. Thus, despite the high level of nest-area fidelity in breeding adults, no genetic isolation was revealed for crested auklets from different parts of the Talan Island colony.