Maritrema portucalensis sp. nov. (Digenea, Microphallidae) from Aveiro estuary, northern Portugal, is described on the basis of excysted metacercariae obtained from the gill lamellae of the shore crab Carcinus maenas (L.). M. portucalensis sp. nov. most closely resembles Maritrema subdolum Jägerskiöld, 1909, a species that also frequently uses C. maenas as second intermediate host. The new species differs from M. subdolum in having a narrower body at the level of testes and a smaller ovary and testes. Also, the digestive caeca presented various folds along their length, thickening in the terminal region. Moreover, the body surface was fully covered by tegumental spines provided with several teeth. To complement our morphological characterization and to identify M. portucalensis metacercariae, the ITS1 rDNA region of the cysts isolated from C. maenas was sequenced and compared with the corresponding available sequences of digenean trematodes belonging to the family Microphallidae. Alignments revealed 28 base-pair differences between the query-ITS1 and that of M. subdolum, and more importantly a 100% similarity with the sequence of Microphallidae sp. no. 15 cercaria from the snail Hydrobia ulvae. The last observation allowed us to establish an unequivocal association between cercaria known as Microphallidae sp. no. 15, and the metacercaria of M. portucalensis sp. nov. characterized in this work, contributing decisively to the clarification of its life cycle.