Currently, 24 species of Encotyllabe Diesing, 1850 (Monogenea: Capsalidae), are recorded as parasites on teleost fishes, but the validity of many species has been questioned due to deficient or incomplete descriptions. Almost all species in the genus have been described from one host species or closely related host species, suggesting host specificity, but some species, specifically Encotyllabe spari Yamaguti, 1934, have been reported from at least 19 species belonging to nine families in two orders (Perciformes and Scorpaeniformes) from Japan, Arabian Gulf and Brazil. Concerning Brazilian records of Encotyllabe spari and Encotyllabe cf. spari, seven species belonging to four families and two orders have been reported as hosts for this species. The aim of this study was to describe two new species of Encotyllabe from Brazil, previously considered as E. spari. Morphological and morphometric (multivariate analysis of proportional measurements standardized by total length) and molecular analysis (LSU rRNA and cox1 gene) were performed in order to identify the collected monogeneans. The description of two new species, namely Encotyllabe bifurcatum n. sp. and Encotyllabe parvum n. sp., parasitizing Pagrus pagrus and Orthopristis ruber, respectively, is the result of the three approaches. The main morphological differences from the most related species include a combination of body size, shape of the male copulatory organ, size and position of the testes. Our results suggest host specificity for members of Encotyllabe and specimens previously recorded as E. spari, other than those from the original description, must be revisited.