Several species of the genus Fissurella coexist on the rocky intertidal substrate in the southeastern coast of the Pacific Ocean. Thirteen species are considered as valid, considering some variable and morphologically unstable species, which have historically allowed registering 58 specific names. This report describes the congruence degree existing between the current typological classification and molecular data obtained from nuclear and mitochondrial genes. Data includes sequences of the spacers ITS1 and ITS2 in the nuclear ribosomal operon and partial sequences of the mitochondrial gene ND1. Reconstruction of phylogenetic relations shows congruence between mitochondrial and nuclear data and allows us to clearly establish two groups of species, including polyphyletic species. The first group contains the `latimarginata complex', which includes morphotypes of F. latimarginata, F. cumingi, F. bridgesii and F. oriens. In addition, the monophyletic species F. radiosa, F. pulchra and F. peruviana are included in this group. The second group corresponds to the complex `costata-picta' that includes F. costata and F. picta. Other monophyletic species in this group were F. maxima in an intermediate position, F. limbata and F. nigra in a basal position. According to our results, F. crassa was situated in a basal position, i.e., close to root, within the phylogenetic tree. This data indicates the necessity of a taxonomic revision of this genus.