The reproductive ecology of Western Palaearctic killifishes is poorly documented and was addressed in this study by investigating, for the first time, two closely related endemic killifish species, namely Aphanius fontinalis and Aphanius saldae. Fish samples were collected monthly from January to October 2017 to test whether the killifishes reproduce simultaneously in the highly alkaline Lake Salda (Turkey). Variation in the mean gonadosomatic index and the frequency of hydrated oocytes indicated that the two species reproduce synchronously from April to September. The timing of reproduction was affected more by day length than by water temperature. Larvae of a parasitic nematode (Eustrongylides sp.) were also observed in the gonadal tissue of some individuals. The effects of parasite infection on basic reproductive parameters were tested in A. fontinalis. Parasite infection had no significant effect on gonad weight, but was associated with significantly decreased fecundity and oocyte diameter. In both species, fecundity was related to fish size; however, the regression model showed non-significant results for the parasite-infected A. fontinalis subsamples. Further research is needed to address the ecological and evolutionary consequences of the coexistence of A. fontinalis and A. saldae and the overlap in breeding seasons.