Mosquitoes serve as vectors for diseases including dengue, Zika, and malaria, for which over half the world's population is at risk. Eliminating those diseases requires intimate knowledge of the eco-evolutionary dynamics of mosquitoes and the pathogens they transmit. Current laboratory and field approaches to interrogate mosquito-pathogen communities, however, are severely limited in throughput preventing a detailed understanding of mosquito-borne disease dynamics. To overcome current limitations, we exploit the fact that biting mosquitoes transmit pathogens by expectorating saliva to autonomously collect saliva droplets resulting from single mosquito bites. Microfluidic analysis of individual saliva droplets enables the high-throughput dissection-free characterization of the genetic make-up of the biting mosquito, and the pathogens it transmits. By integrating this platform with deep sequencing, we aim to provide a panoramic view on the genetic landscape of mosquito-borne viruses undergoing natural transmission cycles. We anticipate that this approach will enhance our understanding of the evolution of mosquito-borne viruses, and may elucidate drivers of mosquito-borne disease emergence.