Vector-borne diseases account for nearly 20% of all globally recognised infectious diseases. Within the spectrum of flea-borne pathogens, Bartonella and Rickettsia bacteria are prominent, contributing to the emergence and resurgence of diseases on a global scale. This study investigates the presence of species of Bartonella and Rickettsia harboured by fleas collected from wild rodents in northwestern Argentina (NWA). A total of 28 fleas from three genera and seven species were assessed. DNA of Bartonella and Rickettsia spp. was found in 12 fleas (42.8%). Phylogenetic analysis of concatenated sequences of gltA and rpoB genes showed the presence of Bartonella quintana in eight fleas of two species, Craneopsylla minerva minerva and Polygenis acodontis. Phylogenetic analysis of concatenated sequences of gltA, ompA and ompB genes identified Rickettsia felis in ten fleas of five species, C. m. minerva, P. acodontis, Polygenis bohlsi bohlsi, Polygenis byturus and Tiamastus palpalis. These bacterial species mark the first report in all flea species studied. This study represents the first survey of flea-borne bacteria for NWA. The results provide information to address strategies for the control and prevention of bartonellosis and rickettsiosis that could have an impact on public health in one of the geographical areas of Argentina with the highest incidence of infections transmitted to humans by ectoparasites.