Between 2012 and 2018 a total of 2094 individual birds representing 265 species (168 passeriformes and 97 non-passeriformes), 70 families (32 passeriformes and 38 non-passeriformes) and 21 orders were sampled for louse-flies and other ectoparasites in different locations in all nine provinces of South Africa. A total of 153 louse-flies of six genera and 16 taxa were recorded: Crataerina acutipennis, Icosta meda, I. minor, I. pilosa, Icosta sp. 1–3, Ornithoica turdi, Ornithoica sp. 1, Ornithomya avicularia, O. biloba, O. fur, Ornithophila metallica, Pseudolynchia canariensis, P. garzettae and Pseudolynchia sp. Louse-flies were found on 137 birds (prevalence 6.5 %) of 78 species from 11 orders. In total we report 93 host-parasite associations of which 84 are reported here for the first time. We found statistically significant higher prevalence and mean abundance of louse-flies in autumn and spring. However, mean intensity was not different between the four seasons. Cases of phoresy of chewing lice, fungal infection and mite infestations of flies are reported and discussed. Available sequences of COI, EF and 16S rRNA genes of examined genera of louse-flies were used in order to assess relative genetic divergence among louse-fly populations.