More than 65 species of the genus Microcotyle Van Beneden & Hesse, 1863, have been described to date, most of them infecting Perciformes. Among the scorpaenoids (Perciformes, formerly Scorpaeniformes) the species of the genus Microcotyle parasitize sebastids and scorpaenids worldwide. In this study, we provide new morphological and molecular data for Microcotyle spp. in sebastids and scorpaenids from the Western Mediterranean and north-east Atlantic. Specimens of Helicolenus dactylopterus (Delaroche, 1809) (n = 107) and Scorpaena spp. (n = 107) were examined and their microcotylid specimens morphologically and molecularly characterized. Microcotyle merche n. sp. ex H. dactylopterus and specimens of Microcotyle algeriensis Ayadi, Gey, Justine & Tazerouti, 2016 from a new host and locality (Scorpaena scrofa from the north-east Atlantic) are herein described. Both species are phylogenetically close, but their morphology is markedly different mostly because the anterior lobe of the haptor present in other Microcotyle species is almost absent in M. algeriensis. Findings of M. merche n. sp. in the Mediterranean also excludes the presence of Microcotyle sebastis in this sea, encouraging the review of the exceptionally large host range and geographical distribution of this species.