The order Polycladida comprises a highly diverse and cosmopolitan group of marine turbellarian flatworms. Owing to the great morphological diversity and the absence of a molecular phylogeny, the classification of this group has always been controversial. Here we seek to add resolution by reporting the results of molecular phylogenetic analysis based on sequences of the 28S ribosomal RNA gene, thus providing a framework for understanding relationships and the evolution of characters within the group. The phylogeny provides strong support for 10 and 7 distinct families within the suborders Acotylea and Cotylea, respectively. In addition, an analysis based on the mitochondrial gene sequences (cytochrome c-oxidase subunit I) reveals further details of the relationships within Acotylea, which were classified by morphological analysis, but not by 28S rRNA sequence-based analyses. These analyses also showed that several species corresponded to previously described genera based on morphological features and character combinations. We conclude that a classification of genera in Acotylea and Cotylea based on molecular phylogeny reflects the morphological diversity of these polyclad flatworms.