Defecation is one of the posterior-station transmission routes for pathogens in haematophagous insects. Culicoides peregrinus Kieffer and Culicoides oxystoma Kieffer (Diptera: Ceratopogonidae) are the proven vectors of many arboviruses, most importantly bluetongue virus, protozoa, and filarial nematodes of livestock. Duration of blood feeding and defecation vary according to species. Culicoides females take blood from their hosts to acquire additional protein to develop their eggs. This study investigates the bacterial communities in defecated contents and gut of the field-collected post-defecated females of C. peregrinus and C. oxystoma. To observe the defecation period and pathogenic bacteria in their defecated contents, engorged females of both species were investigated. The females were transferred to the glass vials containing moistened cotton beds at the bottom and kept in an environmental test chamber. The females defecated within 48 h of post-blood meal intake. The defecated contents discharged by C. peregrinus contained the following bacterial species: Bacillus cereus, Bacillus flexus, Enterococcus faecium, Proteus vulgaris, and C. oxystoma: B. cereus, E. faecium, and Alcaligenes faecalis. Bacillus cereus, B. flexus, Paenibacillus sp., E. faecium, A. faecalis, and Brevundimonas sp. were obtained from the gut of post-defecated females of C. peregrinus, and B. cereus, Lysinibacillus sp., and Paenibacillus sp. were identified from the gut contents of post-defecated females of C. oxystoma. Within the defecated contents, the following pathogenic bacteria, B. cereus, P. vulgaris, and A. faecalis, were detected, which raises the chances of zoonotic posterior transmission to their hosts that should be investigated.