Using 28S ribosomal DNA sequences, we inferred the internal relationships of the order Polycladida. We identified morphological characters for clade support when possible. Monophyletic Acotylea and Cotylea were consistently recovered. In Acotylea, the superfamilies Stylochoidea, Cryptoceloidea and Leptoplanoidea were supported, with Stylochoidea representing the most basal acotylean lineage. In Leptoplanoidea, we united genera lacking a penis armature into the new family Notocomplanidae. Gnesiocerotidae was recovered as the most basal leptoplanoid lineage, and Stylochoplanidae and Notoplanidae were paraphyletic. Among cotyleans, Cestoplanidae, Diposthus popeae + Pericelis spp., Boniniidae, Pseudocerotidae and Prosthiostomidae formed clades. Genera in Euryleptidae were monophyletic, but the family itself was recovered with low support only. The established superfamilies Pseudocerotoidea, Euryleptoidea, Periceloidea and Chromoplanoidea are not supported. Pericelis has been moved to Diposthidae and Pericelidae has been abolished. A clade of Boniniidae + Theama spp. + Chromyella sp. was supported. In Pseudocerotidae, the number of male reproductive structures unites Pseudobiceros and Thysanozoon. Tytthosoceros has been abolished, with all currently described species now placed in Phrikoceros. Our results support several additional synonymies and taxonomic corrections. This new phylogeny provides an increased understanding of relationships in the order and offers a framework for future testing of hypotheses of character evolution and life-history strategies.