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A small population of ancient murrelets (Synthliboramphus antiquus) nests and breeds on vertical sea cliffs in Teuri Island, Japan. Although this small population is at high risk of extinction, practical conservation plans were not established owing to the lack of basic data, for example, ecological and genetic information. Here, mitochondrial DNA and microsatellite analyses were performed on ancient murrelets collected in the Teuri and Aleutian breeding populations, as well as on wintering individuals in Japan and museum specimens. Mitochondrial DNA analysis revealed that the Teuri population shared haplotypes with the Aleutian population, but not with the British Columbian and the Kamchatka populations from a previous study. Microsatellite analysis revealed high gene flow between the Teuri and Aleutian breeding populations. There was no evidence of loss of genetic diversity in the Teuri population. Museum specimens possessed some unique alleles not found in the more recent samples. Our results suggest that strategies for the conservation of Teuri and Aleutian populations should be managed separately from those designed for breeding populations in the eastern Pacific region, at the very least. For conservation of the Teuri population, we do not recommend captive breeding because of gene flow between Teuri and Aleutian populations, but protection of nesting habitats and monitoring of demographic indexes would be more effective for maintaining their genetic diversity and population size. [ABSTRACT FROM AUTHOR]