Little is known about the presence of vector-borne bacteria in southwest Madagascar. Anthropogenic alteration of natural habitats represents an important driver for the emergence of new diseases. Especially the involvement of livestock and the involuntary maintaining of invasive synanthropic animals (particularly rats) facilitate disease transmission from wildlife to humans and associated animals and vice versa. The dissemination or acquisition of ectoparasites is most likely in regions where human/wildlife contact is increasing. Little is known about the presence of vector-borne bacteria in southwest Madagascar. In 2016 and 2017, ectoparasites were collected from various introduced (cattle and goats, cats, dogs and chicken, rats and mice) and native animal species (mouse lemurs [Microcebus griseorufus], Grandidier's mongooses [Galidictis grandidieri], bastard big-footed mice [Macrotarsomys bastardi], greater hedgehog tenrecs [Setifer setosus] and lesser hedgehog tenrecs [Echinops telfairi]) in the northern portion of Tsimanampetsotsa National Park and the adjacent littoral region. Thirteen species of blood-feeding ectoparasites (235 individuals of ticks [5 species], 414 lice [4 spp.] and 389 fleas [4 spp.]) were investigated for the presence and identity of rickettsiae, borreliae, bartonellae and Yersinia pestis using PCR techniques. Rickettsia spp. were detected in every single ectoparasite species (Amblyomma variegatum, A. chabaudi, Rhipicephalus microplus, Haemaphysalis simplex, Argas echinops, Ctenocephalides felis, Echidnophaga gallinacea, Pulex irritans, Xenopsylla cheopis, Haematopinus quadripertusus, Linognathus africanus, L. vituli, Lemurpediculus verruculosus). Lice and ticks were found harboring rickettsiae identified as Rickettsia africae, while Rickettsia felis-like bacteria were associated with fleas. Borrelia spp. were detected in 5% of H. simplex and 1% of R. microplus ticks. Bartonella spp. were detected in 40% of H. quadripertusus pools and in 5% of L. verruculosus pools. Yersinia pestis was detected in X. cheopis and E. gallinacea fleas collected from a rat. This study presents the detection of a broad spectrum of vector-borne bacteria including potential pathogens, and an unexpected finding of Y. pestis far off the known plague foci in Madagascar.