Philophthalmus is a cosmopolitan genus of digeneans that includes ocular parasites of birds and mammals. Despite broad distribution and veterinary importance of these digeneans, there are still gaps in knowledge about their diversity and biology, especially in South America. Herein, we conducted morphological, life cycle, and molecular studies of megalurous cercariae found in aquatic gastropod molluscs Aylacostoma chloroticum and A. tuberculatum collected in the São Francisco River, Brazil. Adult parasites reared experimentally in the eyes of chicks are described here as Philophthalmus aylacostoma n. sp. The new species differs from its congeners known in the Americas by a combination of traits, including the sucker width ratio, the oral sucker to pharynx width ratio, egg size, and the type of vitellarium in adult forms. The new species is morphologically closest to Philophthalmus megalurus, from which it differs by the smaller body and larger eggs, as well as by the measurements of cercariae and the family of snails that act as the intermediate host. Molecular phylogenetic analysis based on 28S rDNA and comparison of cox1 sequences confirm that P. aylacostoma n. sp. is distinct from four previously sequenced named species of the genus. Moreover, cox1 sequences revealed conspecificity of our specimens with an isolate of Philophthalmus sp. previously reported, also in thiarid snails, in Paraná River, Brazil. The interspecific divergence in cox1 between the new species and other species with sequences available for comparison varied between 12 and 15%.