Deep sequencing of small RNAs confirms an annelid affinity of Myzostomida

► Deep sequencing of Myzostoma cirriferum small RNAs provided 31.221 sequences annotated as miRNAs. ► Myzostomids bear 13 annelid specific miRNA-families, supporting an annelid origin of these enigmatic protostomes. ► Using secondary structure predictions 20 new miRNA-candidates have been identified for Myzostomida.