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Background  Biting midges of the genus  Culicoides  (Diptera: Ceratopogonidae) transmit pathogens that cause important diseases. No effective technique has been found to properly control either  Culicoides  spp. abundance or their likelihood to transmit pathogens. Endosymbionts, particularly  Wolbachia , represent powerful alternatives to control arthropods of health interest. In arthropods,  Wolbachia  can reduce vector fitness and vector’s pathogen transmission capacity, thus being a potential target for population reduction and replacement strategies.    Results  The presence of  Wolbachia  and  Cardinium  endosymbionts was screened in Spanish  Culicoides  spp. populations at livestock premises and natural habitats. The first detection of  Wolbachia -infected  Culicoides  spp. in Europe is reported. The putative Palaearctic vectors for bluetongue and Schmallenberg diseases,  C. imicola ,  C. obsoletus  ( s . s .) and  C. pulicaris  ( s . l .), were infected with  Wolbachia . Four genetic clusters of closely-related  Wolbachia  strains from A and B supergroups were detected infecting  Culicoides. Cardinium  strain of the C-group was detected in  C. obsoletus  ( s . l .). Both endosymbionts,  Wolbachia  and  Cardinium , were detected in  Culicoides  species of minor epidemiological relevance as well. Higher prevalence of  Wolbachia  infection was detected in natural habitats, while livestock premises lead to higher prevalence of  Cardinium . Significant differences in the prevalence of  Wolbachia , but not  Cardinium , were also detected between some  Culicoides  species and between locations.    Conclusions  The presence of  Wolbachia  and  Cardinium  endosymbionts in  Culicoides  is expected to trigger new research towards the control of  Culicoides -transmitted diseases. The results of the present study could have an impact beyond the  Culicoides  arena because successful  Wolbachia  transfection is possible even across genus and species barriers.    Electronic supplementary material  The online version of this article (10.1186/s13071-017-2486-9) contains supplementary material, which is available to authorized users.

parasites and vectors

First detection of Wolbachia-infected Culicoides (Diptera: Ceratopogonidae) in Europe: Wolbachia and Cardinium infection across Culicoides communities revealed in Spain