Study of population genetic structure is essential for insight in species biology, but mechanisms of its formation and factors influencing it remain insufficiently understood. Here we analyzed differentiation among populations in small colonial seabird of North Pacific, the Parakeet Auklet Aethia psittacula, which was previously considered as a monomorphic species. We compare our results with data on congeneric species to investigate the most important factors affecting the process of population differentiation in Aethini. We analyzed morphometric measurements, mitochondrial DNA control region fragment and microsatellite loci from six Parakeet Auklet colonies spanning the breeding range. Although results of microsatellite variability analysis did not reveal differences between birds from different colonies, results of control region variability and morphometric analyses testified for a slight but significant differentiation between birds from the Aleutian Islands and other parts of their range. They were significantly smaller in most linear parameters measured and had higher body condition (expressed as the scaled mass index). The results of mtDNA analysis and discrepancy between different types of genetic markers indicated that birds from Aleutian Islands and from the other parts of their breeding range probably originated from different refuges and the differentiation of mitochondrial lineages between them took place around 100 000 years ago. Our results and conclusions from the comparison with congeneric species indicated that foraging and migration patterns seem to determine population structure in small planktivorous alcids, with panmixia in highly mobile species, clear population differentiation in resident species and intermediate population differentiation in more dispersive species.