We present details on bat flies of the families Nycteribiidae and Streblidae parasitising an endemic Malagasy fruit bat, Rousettus madagascariensis, including aspects of species diversity, rates of parasitism and sex ratios. Data were collected from 639 bats occupying the same cave day roost site in the Parc National d'Ankarana, extreme northern Madagascar, and visited on three occasions: end of dry season (September 2014 and September 2015) and during the rainy season (January 2015). From a collection of over 3500 bat flies, two species were identified — Eucampsipoda madagascarensis (n = 3227) of the family Nycteribiidae and Megastrebla wenzeli (n = 350) of the family Streblidae. The number of E. madagascarensis per bat host showed seasonal variation with a notable reduction during the rainy season. The sex ratio of E. madagascarensis was significantly biased towards males, and this pattern was more pronounced during the dry season. In comparison, M. wenzeli, which were distinctly less common, showed statistical differences between the three site visits in prevalence, but not for the number of parasites per host. For E. madagascarensis parasitism rates varied with age and sex, with adult male R. madagascariensis having more ectoparasites than females, subadults and neonates, while no difference in parasitism rate was found for M. wenzeli based on host age and sex.