Data generated to investigate the hybridization between sea turtles species in Abrolhos Archipelago, Brazil. The data showed that there are first-generation hybrid females nesting in Abrolhos, resulting from crossings between hawksbill males (Eretmochelys imbricata) and loggerhead females (Loggerhead turtle), and backcrossed hatchlings from both parental species. The reproductive output data of Abrolhos nests suggests a disadvantage of hybrids when compared to loggerheads. For the first time, we have shown the association between hybridization and low reproductive success, which may represent a threat to sea turtle conservation.