During the past twenty years, a number of molecular analyses have been performed to determine the evolutionary relationships of Onchocercidae, a family of filarial nematodes encompassing several species of medical or veterinary importance. However, opportunities for broad taxonomic sampling have been scarce, and analyses were based mainly on 12S rDNA and coxI gene sequences. While being suitable for species differentiation, these mitochondrial genes cannot be used to infer phylogenetic hypotheses at higher taxonomic levels. In the present study, 48 species, representing seven of eight subfamilies within the Onchocercidae, were sampled and sequences of seven gene loci (nuclear and mitochondrial) analysed, resulting in the hitherto largest molecular phylogenetic investigation into this family. Although our data support the current hypothesis that the Oswaldofilariinae, Waltonellinae and Icosiellinae subfamilies separated early from the remaining onchocercids, Setariinae was recovered as a well separated clade. Dirofilaria, Loxodontofilaria and Onchocerca constituted a strongly supported clade despite belonging to different subfamilies (Onchocercinae and Dirofilariinae). Finally, the separation between Splendidofilariinae, Dirofilariinae and Onchocercinae will have to be reconsidered. Filariae are predominantly tissue-dwelling nematodes of the Onchocercidae (Spirurida). They are parasites of terrestrial vertebrates and some of them are particularly well known as agents of human diseases in tropical environments (e.g. onchocercosis, lymphatic filariosis, loaosis). Because of their predilection for host tissue sites, filariae are difficult to collect and their diversity is far from being well-investigated. Given the lack of fossilized material, it is not possible to formulate a comprehensive evolutionary hypothesis for this group based exclusively on morphological studies. Molecular analyses on the other hand have so far been based on a limited number of filarial species only or have used genetic markers convenient for species differentiation but not for retracing filarial history. Thus a consistent evolutionary framework for this family is still not in place. The originality and strength of the present study rest within its ability to access an unusually large range of biological samples, comprising 48 species representing seven of the eight onchocercid subfamilies. Using a new multi-gene dataset analysis, five major clades within the family were defined, including i) a group of ancestrally-derived subfamilies, ii) Setariinae as a sister group to all remaining subfamilies and iii) one large clade comprising genera of the Dirofilariinae, Onchocercinae and Splendidofilariinae.