Thysanoptera is one of the insect orders with approximately 6000 described species distributed around the world. Nearly 93% of the recognized species in the order are grouped into two large families, Phlaeothripidae and Thripidae, while the remaining species distributed in seven smaller families. The Aeolothripidae, as the third largest family in the order, comprises about 5 % of the total species of Thysanoptera. Parallelly, Melanthripidae is one of the small families that, until recently, was considered to be a subfamily in the family Aeolothripidae. The Merothripidae is another small family comprising fungus feeding species in warmer parts of the world. In order to determine phylogenetic relationships among these three families (Aeolothripidae, Melanthripidae and Merothripidae) as well as some main genera of the first two families, 192 morphological characters of the adult thrips were selected. A species of family Stenurothripidae was considered as outgroup. The data matrix was analyzed by parsimony method using PAUP* 4.0a152. The created matrix included the information of 59 species from 13 genera; i.e. 33.3% of the genera of the family Aeolothripidae, 75% of the genera of the family Melanthripidae and 14% of the genera of the family Merothripidae. The data in the phylogenetic studies provided strong support for the monophyly of each family. Furthermore, Aeolothripidae considered as a sister group of Melanthripidae while both were recovered as a sister group of the family Merothripidae. Although the monophyly of three genera, Aeolothrips, Cranothrips and Desmothrips, was not confirmed, but the morphological data tend to support monophyly of the genera Melanthrips and Rhipidothrips. Moreover, it was found that two species of different genera, Aeolothrips albicinctus and Desmothrips reedi are more close to each other than to any other species of their own genera. The genus Ankothrips was recovered as a sister group of the clade “Melanthrips and Cranothrips”, and showed the correct classification of Ankothrips within the family Melanthripidae.