During the last decade, many morphotypes of larval forms of Hysterothylacium have been proposed; however, their boundaries are taxonomically unclear. We compare newly collected material with data available for Hysterothylacium larvae, based on genetics and morphology, in order to evaluate their relationships and simplify their classification. The previously described Hysterothylacium larval type IV, type V, and type X were found in several marine fishes from Brazil. A new Hysterothylacium larval type XV, parasitic in Elops saurus from State of Sergipe, north-eastern Brazil, was proposed based on its genetic singularity and the presence of numerous spines throughout the body. Based upon phylogenetic reconstruction using the ribosomal DNA (rDNA) ITS2 sequences along with morphological traits, the following third stage larvae were considered valid (synonyms are inside parenthesis) type III (= types VII and VIII), type V (= types VI, XII, and XIII), and type X (= type XIV). Despite the lack of molecular data, Hysterothylacium larval type II is considered as synonym of type I because of their identical morphology. The morphometry of Hysterothylacium third stage larvae proved to be weak as a diagnostic tool due to its high rates of variation. Phylogenetic reconstruction using the concatenated sequences of rDNA ITS1-5.8S-ITS2 and the mitochondrion DNA (mtDNA) cox2 revealed that the sampled Hysterothylacium larval types V may represent three different species and H. deardorffovestreetorum may represent two different taxa. Furthermore, H. deardorffovestreetorum is considered species inquirenda due to its problematic description and diagnosis which are based only on larvae. A key to Hysterothylacium larvae from marine fishes is provided.