The genetic background of individual mosquito species and populations withi
n those species influences the transmission of mosquito-borne pathogens to
humans. Technical advances in contemporary genomics are contributing signif
icantly to the detailed genetic analysis of this mosquito-pathogen interact
ion as well as all other aspects of mosquito biology, ecology, and evolutio
n. A variety of DNA-based marker types are being used to develop genetic ma
ps for a number of mosquito species. Complex phenotypic traits such as vect
or competence are being dissected into their discrete genetic components, w
ith the intention of eventually using this information to develop new metho
ds to prevent disease transmission. Both genetic- and physical-mapping tech
niques are being used to define and compare genome architecture among and w
ithin mosquito species. The integration of genetic- and physical-map inform
ation is providing a sound framework for map-based positional cloning of ta
rget genes of interest. This review focuses on advances in genome-based ana
lysis and their specific applications to mosquitoes.