Molecular polymorphism of six species of Thysanoptera of both sexes, collected from different locations and host plants in Hungary was studied by using RAPD-PCR technique. The specimens were classified according to sampling sites (Gödöllö, Nagykovácsi and Valkó), host plants (Lathyrus tuberosus, Medicago sativa, Taraxacum officinale, Trifolium pratense), sexes, and larvae in case of Aeolothrips intermedius. On the basis of the total of 103 fragments generated by 15 RAPD primers the genetic distances were calculated by cluster analysis using simple matching method. The dendrogram resulted in two main groups: Aeolothripidae (Aeolothrips intermedius) and Thripidae (Frankliniella intonsa, Kakothrips robustus, Odontothrips confusus, Thrips dilatatus and T. tabaci). Within the family Thripidae two subgroups were observed including (i) F. intonsa, T. dilatatus and T. tabaci, and (ii) K. robustus and O. confusus. Two population-specific and one sex-linked fragments were identified by the RAPD primers, OPQ 14, NO11 and OPA08, respectively.