DNA sequence variation from two nuclear introns and part of the mitochondrial cytochrome-b gene were used to Evaluate population structure among three subspecies of Least Term that nest in the United States (California [Sterna antillarum browni], Interior [S. a. athalassos], Eastern [S. a. antillarum]). Sequence variation was highest for nuclear intron XI (Gadp) within the glyceraldehyde-3-phosphate dehydrogenase gene. The second nuclear intron was fixed for the same allele in all subspecies. Fixation indices, FST and MST, for Gadp indicated genetic divergence between California and Interior subspecies. Estimates of nuclear gene flow were <4 individuals/generation, except between the Interior and Eastern subspecies (4 individuals/generation). Genetic indices for mitochondrial DNA did not differ among subspecies, and gene flows (reflecting female dispersal) ranged from 10 to 83 individuals/generation. Reservations are expressed about the validity of the current subspecific divisions and further research is required, including their taxonomic relationship to the Little Tern (Sterna albifrons).