A phylogenetic analysis of Heterotermes from 63 locations in the West Indies and associated mainland is presented based on the DNA sequence of a portion of the mitochondrial 16S rRNA gene. Maximum parsimony analysis of the aligned Heterotermes species and the outgroup taxa resulted in a consensus tree with five distinct West Indian groups. Morphological characters and geographical distribution supported the resulting clades, which were given the following taxonomic assignments: Heterotermes cardini (Bahamas and Cuba); Heterotermes sp. (Bonaire, FL; Grand Cayman; Grand Turk; Jamaica; and St. Barthelemy), Heterotermes convexinotatus (Antigua, Barbados, Curacao, Dominican Republic, Martinique, Puerto Rico, St. Kitts, St. Maarten, Venezuela, and Virgin Island), and Heterotermes tenuis (Lesser Antilles except Barbados and Martinique, Ecuador, and Suriname). The Florida Heterotermes sp. is a known nonendemic population, whereas those on Barbados, Grand Cayman, Grand Turk, Martinique, St. Barthelemy, and elsewhere may harbor or consist solely of nonendemic populations.