Infections by Rhizopus spp. account for about 90% of zygomycoses, many of which are lethal in immunocompromised patients. We recently noted that several strains of Rhizopus microsporus harbour rare bacterial endosymbionts (Burkholderia sp.) for the production of 'mycotoxins', which might play a role as virulence factors in human Rhizopus infections. In this study eight clinical Rhizopus spp. isolates have been investigated for the presence of toxin-producing bacterial endosymbionts. By metabolomic data, PCR targeting bacterial 16S rDNA and microscopic investigations with fluorescence dyes we provide three lines of evidence showing that the fungal strains are not associated with endofungal bacteria. Consequently, toxin-producing bacteria are not essential for Rhizopus infections and the development of zygomycoses in humans.