Results of analyses of molecular sequence (COI, 28S-D2) and morphology (21 character states) data, both alone and combined, were used to determine relationships between 18 species of Scirtothrips (Thysanoptera: Thripidae, Thripinae). Two species of Neohydatothrips from Panama were used as the outgroup. Five major pest Scirtothrips were included in these analyses: S. aurantii, S. citri, S. dorsalis, S. kenyensis, and S. perseae. Trees generated from a parsimony analysis of molecular data and Bayesian analysis of molecular and morphology data combined showed high levels of congruence. The morphology-only tree had several differences in species groupings when compared with trees derived using molecular data. Both parsimony and Bayesian analyses using molecular data indicated that Scirtothrips species associated with avocados were monophyletic, a result not observed with morphological analyses. No support was found for a monophyletic S. dorsalis clade when sampled from six different countries. The S. dorsalis complex may be comprised of at least three separable groups identifiable at the molecular level, but indistinguishable morphologically. The implications of this finding for S. dorsalis, a thrips pest of global significance with high invasion potential, are discussed.