Hippocrepis hippocrepis is a notocotylid that has been widely reported in capybaras; however, the molluscs that act as intermediate hosts of this parasite remain unknown. Furthermore, there are currently no molecular data available for H. hippocrepis regarding its phylogenetic relationship with other members of the family Notocotylidae. In the present study, we collected monostome cercariae and adult parasites from the planorbid Biomphalaria straminea and in the large intestine of capybaras, respectively, from Belo Horizonte, Minas Gerais, Brazil. We subjected them to morphological and molecular (amplification and sequencing of partial regions of 28S and cox-1 genes) studies. Adult parasites collected from the capybaras were identified as H. hippocrepis and the sequences obtained for both molecular markers showed 100% similarity with monostome cercariae found in B. straminea. The sequences obtained for H. hippocrepis were compared with data available in public databases; analysis revealed this species differs from other notocotylids with available sequences (1.5-3.8% with respect to 28S and 11.4%-13.8% with respect to cox-1). On the phylogenetic analyses, H. hippocrepis appeared to be a distinct lineage in relation to other notocotylids. Some ecological aspects related to the infection of capybaras with H. hippocrepis are briefly discussed.