Background: Wolbachia sp. is an endosymbiotic bacterium that is widespread among arthropods and filarial nematodes. It affects the fertility and maturation of its arthropod hosts, which in some cases are vectors of infectious diseases of humans and animals. Acanthocheilonema reconditum is a canine filarial nematode, which can eventually infect humans through arthropods. An outbreak of A. reconditum has been reported recently in dogs in the southwest of Colombia, specifically in Cali. In addition, Wolbachia sp. is currently used for the biological control of the mosquito Aedes egypti in cities in the north and south-west of Colombia. Aedes egypti is a vector of dengue fever, a major public health disease in tropical and subtropical areas of the world. The objectives of this study were to detect Wolbachia sp. in mosquito and flea samples collected from dogs in southwestern Colombia and to determine the co-infection of Wolbachia sp. and A. reconditum in the recent outbreak of canine filariasis in Santiago de Cali. Methods: A total of 18 mosquitoes of the genera Aedes and Culex and 18 Ctenocephalides felis fleas were collected in Santiago de Cali and nearby municipalities. DNA was extracted and 16S rRNA and ftsZ gene fragments were identified using conventional and nested polymerase chain reaction. In addition, the presence of Wolbachia sp. was analyzed in 55 cases positive for A. reconditum previously detected in the city, using the same molecular techniques. Results: From the analysis of 18 mosquitoes and 18 fleas, using molecular techniques based on the 16S rRNA and ftsZ genes, Wolbachia sp. was detected in all the arthropods analyzed. Wolbachia sp. was not detected in the samples obtained from dogs infected with A. reconditum. Conclusions: Molecular analyses were shown to be effective for the identification of Wolbachia sp. in mosquitoes and fleas but not in samples positive for A. reconditum.