Marbled Murrelets (Brachyramphus marmoratus) are coastal seabirds that breed predominantly in old-growth forest throughout the North Pacific. Presently they are classified into two phenotypically distinct subspecies: one in North America (B. m. marmoratus) and one in Asia (B. m. perdix). The Asian form was classified as a separate species in 1811, but was lumped with B. marmoratus during the 20th century. Populations of both types are considered threatened or endangered and information about the extent of genetic differentiation among birds from different sites is required for their conservation. We compared variation in 1,045 base pairs of the mitochondrial cytochrome b gene and 39 allozyme loci among Marbled Murrelets and the closely related Kittlitz's Murrelets (B. brevirostris) from throughout the North Pacific. All analyses indicted that North American and Asian Marbled Murrelets are genetically distinct: cytochrome b sequences were highly divergent, fixed allele differences occurred at two allozyme loci, and estimated gene flow was essentially zero. Phylogenetic analyses of cytochrome b sequences and allozymes both provided strong support for a monophyletic relationship among North American Marbled Murrelets and Kittlitz's Murrelets, with Long-billed Murrelets forming the basal lineage. Long-billed and North American Marbled Murrelets clearly represent distinct species by any definition, and must be managed independently. Significant genetic differentiation also was found among both Marbled and Kittlitz's Murrelets from different sites within North America.