Vector-borne illnesses account for nearly 20% of all globally recognised infectious diseases. Within the spectrum of pathogens transmitted by fleas, Bartonella and Rickettsia bacteria are prominent, contributing to the emergence and resurgence of diseases on a global scale. This study aimed to investigate the presence of specific strains of Bartonella and Rickettsia species harboured by fleas collected from wild rodents in Northwestern Argentina. 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 marking the first report in all flea species studied. This study represents the first survey of flea-borne bacteria for Northwest Argentina. 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.