Mosquitoes are responsible for the transmission of pathogens that cause disease in over 400 million people each year worldwide. The capacity to transmit disease-causing pathogens can differ greatly between different species of the same genus or even populations of the same species. The geographic distribution and prevalence of vector-borne diseases is proportional to the distribution and prevalence of the relevant mosquito vectors. Furthermore, vector-borne pathogens can differ greatly in virulence and drug-resistance attributes. Accurate and rapid identification and discrimination of vector mosquito species and the pathogens they transmit are, therefore, essential components of disease prevention and control strategies, as well as of epidemiological and ecological research studies. Here, we review advances in diagnostic methods and tools for both vectors and pathogens which cause human disease.