Previous molecular phylogenetic studies have focused on either the relationship between isopteran families or among species within a given genus, but there are presently few studies focusing on individual families and no known molecular studies for Rhinotermitidae. We examined 38 rhinotermitid species representing 10 genera, relative to representatives of four other isopteran families. Sequencing of a 667-base pair region of the mitochondrial DNA cytochrome oxidase II gene revealed 343 polymorphic sites within the family. Tajima-Nei genetic distances ranged from 11 to 23% among rhinotermitid genera. Maximum parsimony and maximum likelihood analysis of DNA sequences support existing hypotheses that Mastotermitidae is the basal lineage among extant termites, and the family Rhinotermitidae is polyphyletic given the current familial status of Serritermitidae. DNA sequence data suggest that Serritermitidae should be relegated to the subfamily Serritermitinae, as proposed by Emerson in 1965.