Conservation plans for the North Pacific Coast are beginning to acknowledge that the old-growth forests remaining on the extensive archipelagos of the region may require a new management paradigm. Extensive timber harvesting activities on these islands may impact wildlife populations and be particularly detrimental to the large number of endemics. Because insular biotas have suffered a disproportionate number of documented extinctions worldwide, the documentation of taxonomic validity and spatial distribution of endemics should be a priority for management efforts. To date, few North Pacific coastal endemics have been reevaluated since their original descriptions. This study provides an independent view of endemism in the Alexander Archipelago of southeast Alaska through a phylogeographic assessment of eight species of mammals ( Sorex monticolus, Glaucomys sabrinus, Microtus longicaudus, Clethrionomys rutilus, Clethrionomys gapperi, Martes americana, Mustela erminea, Ursus americanus). The molecular data (mitochondrial sequence variation of the cytochrome b gene) suggest a dynamic history of faunal interchange in the region. While some purported endemics show minimal levels of genetic divergence from other conspecific populations, other taxa appear to be more divergent than recognized by current taxonomy. Some species in the region are comprised of multiple clades or evolutionarily significant units. These reciprocally monophyletic lineages may be the result of multiple Holocene invasions (neoendemics) or they may have persisted in refugia (paleoendemics) in the region during Pleistocene glacial advances. This emerging historical perspective should have direct implications for the management of these endemic taxa.