Strong epidemiological evidence suggests that onchocerciasis may be associated with epilepsy-hence the name onchocerciasis-associated epilepsy (OAE). However, the pathogenesis of OAE still needs to be elucidated, as recent studies have failed to detect in the central nervous system of persons with OAE. Therefore, it was suggested that a potentially neurotropic virus transmitted by blackflies could play a role in triggering OAE. To investigate this hypothesis, adult blackflies were collected in an onchocerciasis-endemic area with a high OAE prevalence in the Ntui Health District, Cameroon. A viral particle-based shotgun sequencing approach was used to detect viral sequences in 55 pools of 10 blackflies. A very high abundance of viral reads was detected across multiple (novel) viral families, including viral families associated with human disease. Although no genomes closely related to known neurotropic viruses were found in the blackfly virome, the plethora of novel viruses representing novel species, genera and even families warrant further exploration for their potential to infect vertebrates. These results could serve as a first step for studying the viruses associated with the haematophagous blackfly, which also could be present in their nematode host . Exploring the diversity of viruses in blackflies should be included in the active surveillance of zoonotic diseases.