Pygocentrus piraya is an endemic species of the São Francisco River basin. In this study, 342 carnivorous fish were examined, nymphs specimens of Sebekia sp. and its ecological indexes are recorded only in piranhas, of the total of 53 collected from three marginal lagoons of the middle São Francisco River basin: 17 specimens from Curral de Varas lagoon; 15 from Maris lagoon, both of state of Minas Gerais; and 21 specimens from Mocambo lagoon, state of Bahia. The prevalence (P) and mean abundance (MA) of Sebekia sp. nymphs in intermediate hosts were as follows: in Curral de Varas lagoon, P = 11.8%, MA = 0.18; in Maris lagoon, P = 46.6%, MA = 0.47; and in Mocambo lagoon, P = 14.3%, MA = 1.05. Despite the lower number of fish examined from Maris lagoon, this lagoon had the highest number of piranhas (seven) parasitized by Sebekia sp. Pentastomids have zoonotic importance and evaluation of the indirect life cycle of sebekids in lagoons is necessary for defining the intermediate and final hosts involved. This record is novel and stems from collection of piranhas in the marginal lagoons of the São Francisco River, in the states of Minas Gerais and Bahia, Brazil.