The taxonomy of clupeiforms has been extensively studied, yet phylogenetic relationships among component taxa remain controversial or unresolved. Here we test current and new hypotheses of relationships among clupeiforms using mitochondrial rRNA genes (12S and 16S) and nuclear RAG1 and RAG2 sequences (total of 4749bp) for 37 clupeiform taxa representing all five extant families and all subfamilies of Clupeiformes, except Pristigasterinae, plus seven outgroups. Our results, based on maximum parsimony, maximum likelihood, and Bayesian analyses of these data, show that some traditional hypotheses are supported. These include the monophyly of the families Engraulidae, consisting of two monophyletic subfamilies, Engraulinae (Engraulis and Anchoa) and Coilinae (Coilia and Setipinna), and Pristigasteridae (here represented only by Ilisha and Pellona). The basal position of Denticeps among clupeiforms is consistent with the molecular data when base compositional biases are accounted for. However, the monophyly of Clupeidae was not supported. Some clupeids were more closely related to taxa assigned to Pristigasteridae and Chirocentridae (Chirocentrus). These results suggest that a major revision in the classification of clupeiform fishes may be necessary, but should await a more complete taxonomic sampling and additional data.