We assessed phylogeographic history of moose Alces alces in southeastern Alaska, USA, by determining their genetic affinity to surrounding populations thereby clarifying their origin and uncertain taxonomic status. Moose from central and southern regions of the southeastern Alaska panhandle were characterized by two mitochondrial haplotypes that were highly divergent from those in the remainder of the state; overlap with other haplotypes occurred only in the northernmost area of the panhandle. Moose inhabiting areas of British Columbia, Canada, immediately adjacent to Alaska's panhandle showed high haplotype diversity. A small proportion of those moose shared haplotypes with moose in southeastern and interior Alaska, but most possessed haplotypes that were restricted to that region. Association between geographic distribution and phylogenetic structure of haplotypes indicated spatial separation of moose lineages in the past. Our results indicate that there were two separate entries of moose into the region during colonization, likely from different geographic areas. Coastal populations of moose living south of 58°45′N latitude in southeastern Alaska should be classified as A. a. andersoni rather than as A. a. gigas. Behavioural and morphological differences between A. a. gigas and other forest-dwelling subspecies in North America indicate a need to examine moose management strategies and objectives in southeastern Alaska.