The echinoderm symbionts Myzostomida are marine worms that show an enigmatic lophotrochozoan body plan. Historically, their phylogenetic origins were obscured due to disagreement about which morphological features are evolutionarily conserved, but now most morphological evidence points to annelid origins. In contrast, recent phylogenetic analyses using different molecular markers produced variable results regarding the position of myzostomids, but all suggested these worms are not derived annelids. To reexamine this issue, we analyzed data from nuclear genes (18S rDNA, 28S rDNA, Myosin II, and Elongation Factor-1alpha), and a nearly complete myzostomid mitochondrial genome. Here, we show that the molecular data are in agreement with the morphological evidence that myzostomids are part of the annelid radiation. This result is robustly supported by mitochondrial (gene order and sequence data) and nuclear data, as well as by recent ultrastructural investigations. Using Bayes factor comparison, alternative hypotheses are shown to lack support. Thus, myzostomids probably evolved from a segmented ancestor and gained a derived anatomy during their long evolutionary history as echinoderm symbionts.