The order Thysanoptera (Insecta: Paraneoptera), commonly known as thrips, includes organisms that exhibit a wide range of social and feeding behaviors that are of particular interest in evolutionary studies. These studies within thrips have been inhibited by the lack of knowledge of thrips relationships. The recognized classification scheme strives to reflect evolutionary relationships and is based upon morphology. Molecular data is next as morphology alone is not enough to resolve relationships. Few molecular studies have been conducted and all were limited in their taxon sampling and genetic sampling. To provide a foundation of future evolutionary studies, the objectives of this study are to (1) test the monophyly of the suborders Terebrantia and Tubulifera, (2) test the monophyly of the families and decipher their relationships, and (3) test the monophyly of the recognized subfamilies. Phylogenies were reconstructed based upon 5299 bp, from five genetic loci: 18S ribosomal DNA, 28S ribosomal DNA, Histone 3 (H3), Tubulin-alpha (TubA) and cytochrome oxidase c subunit I (COI). 99 thrips species from seven of the nine families, all six subfamilies and 70 genera were sequenced. Maximum Parsimony (MP), Maximum Likelihood (ML) and Bayesian analysis all strongly support a monophyletic Tubulifera and Terebrantia. Phlaeothripidae, Aeolothripidae, Melanthripidae and Thripidae are all monophyletic families. The relationship between Aeolothripidae and Merothripidae to the rest of Terebrantia is equivocal. Morphological and molecular data suggest Aeolothripidae or Merothripidae could be the basal lineage of Terebrantia. Four of the six subfamilies are recovered as monophyletic. The two largest subfamilies, Phlaeothripinae and Thripinae, are paraphyletic and require further study to understand relationships within them.