Myzostomida comprise a group of marine worms associated mainly with echinoderms since the Carboniferous. Due to their unusual morphology the phylogenetic position in relation to other Lophotrochozoa is discussed since their description. According to different morphological and molecular markers the Myzostomida are either close to Platyzoa or Annelida. Here we investigated small non-coding RNAs of Myzostoma cirriferum to infer the phylogenetic position of myzostomids. Based on transcriptomic data collected by Illumina Deep Sequencing we analyzed the microRNA (miRNA) families occurring in M. cirriferum. Phylogenetic analysis revealed the presence of 13 miRNA-families exclusively shared by Annelida (including Sipuncula) and Myzostomida, as such highly significantly supporting an annelid origin of myzostomids. Furthermore, using a mapping-approach and secondary structure models we predicted several miRNA-candidates unique for myzostomids.