The microphallid Maritrema eroliae parasitizes shore birds in marine ecosystems while its larval stages infect mud snails and crustacean hosts. Because it is difficult to morphologically distinguish between larvae of M. eroliae and other microphallids cooccurring in the same habitat, partial nucleotide sequences of the ribosomal DNA (rDNA), including the 28S and 18S in addition to complete sequences of ITS1 and ITS2, were scrutinized. This analysis was used to establish the snail-crab link in the life cycle of M. cf. eroliae. The rDNA 28S, 18S, and ITS sequences of metacercariae from the crab Xantho exaratus and sporocysts from the snail Clypeomorus bifasciata were compared. Sequence alignment demonstrated that the sporocyst and metacercaria may belong to M. eroliae and suggested a new second intermediate host for M. eroliae, the crab X. exaratus. The phylogenetic positions of the larval stages were determined by comparing the 28S, 18S, and ITS sequences with those of other trematodes available in GenBank. The phylogenetic trees confirmed the position of M. cf. eroliae within the Microphallidae and found it to be closely related to Maritrema heardi and Maritrema neomi. The present study represents the first molecular study correlating the larval stages in the life cycle of M. cf. eroliae using partial sequences of 28S and 18S in addition to complete ITS1 and ITS2 sequences. Furthermore, the sequences elucidated the evolutionary relationship of M. cf. eroliae to other microphallids.