The doubly uniparental mode of inheritance, characteristic of the Mytilidae, consists of an F-type mitochondrial lineage transmitted only through females and an M-type lineage present only in male gonads and therefore transmitted only through males. In this work, we search for evidence of two mitochondrial lineages in Perna perna by studying the same 16S rRNA region that allowed for the discovery of doubly uniparental inheritance in the Mytilus group and in one venerid clam. The region was screened for substitutions using eight restriction enzymes to analyze two kinds of tissues (somatic and gonadal) from 20 males and 20 females from the south of Brazil. A restriction map was constructed after confirming restriction sites with sequence analysis. After amplification with the same primers used in previous studies, a fragment of 517 bp was obtained, which was 10 bp shorter than the one from Mytilus species. No variation was found among individuals or between sexes or kinds of tissue (gonadal and somatic). The absence of variation in this region was confirmed by sequence analysis, and this result left us unable to reject the hypothesis of common maternal mitochondrial inheritance. The 16S rDNA sequence obtained for Perna perna was aligned with twenty-three representative sequences from fifteen mytilid species available in GenBank, and a neighbor- joining tree was constructed. The phylogenetic analysis showed all Perna species clustered together in a single branch, which was supported 100% by bootstrap analysis and was more closely related to the branch of the Mytilus group than the other representative genera of the Mytilidae.