Graduation date: 2007Historically, least terns (Sterna antillarum) were one of the most common tern species in North America. However, population declines have resulted from direct and indirect anthropogenic pressures on their breeding and foraging habitat. Three subspecies of least terns have been described within the United States: California least tern (S. a. browni), Interior least tern (S. a. athalassos), and East Coast least tern (S. a. antillarum). California and Interior subspecies are listed as endangered under the U.S. Endangered Species Act. However, the taxonomic status of least terns is a highly contentious issue which has implications for setting conservation priorities at erroneous levels of taxonomic distinctness. Thus, understanding population structure and taxonomy is critical for successful conservation of least terns. To clarify the phylogeographic patterns and population structure and evaluate the traditional subspecific designations, we examined variation in two mitochondrial DNA (mtDNA) genes and 10 microsatellite loci among least terns in North America. MtDNA control region sequences and 10 polymorphic microsatellite loci were used to evaluate traditional subspecific designations and genetic structure in least terns. While highly variable, results from mtDNA control region sequences and microsatellite loci did not support the three traditional subspecies that occur in the United States. However, mtDNA pairwise θST comparisons and AMOVA analyses indicated some genetic structure between the California and the remaining Interior/East Coast breeding areas indicating restriction to female-mediated gene flow. We evaluated phylogeographic patterns and demographic history of least terns using the mtDNA NADH dehydrogenase subunit 6 (ND6) sequences. Phylogeographic analysis revealed no association with geography or traditional subspecies designations. Population genetic analysis did reveal slight genetic differentiation between the California breeding areas and all other Interior/East Coast breeding areas. ND6 data indicate least terns have undergone a recent population expansion. Temporal comparisons between four contemporary breeding areas and their historical counterparts found significant difference in nucleotide diversity and seven historical haplotypes were absent from contemporary breeding areas suggesting loss of genetic diversity. This study is the most comprehensive evaluation of the genetic status of least terns, or any tern species, to date. It points to the need for better information on breeding site fidelity and natal philopatry across the species range was well as population-specific movements throughout the annual cycle. These finding should provide a helpful perspective to those planning conservation efforts throughout the species range.