The process of colonizing any arthropod species, including vector mosquitoes, necessarily involves adaptation to laboratory conditions. The adaptation and evolution of colonized mosquito populations needs consideration when such colonies are used as representative models for pathogen transmission dynamics. A recently established colony of Anopheles darlingi, the primary malaria vector in Amazonian South America, was tested for genetic diversity and bottleneck after 21 generations, using microsatellites. As expected, laboratory An. darlingi had fewer private and rare alleles (frequency < 0.05), decreased observed heterozygosity, and more common alleles (frequency > 0.50), but no significant evidence of a bottleneck, decrease in total alleles, or increase in inbreeding compared with field specimens (founder population). Low-moderate differentiation between field and laboratory populations was detected. With these findings, and the documented inherent differences between laboratory and field populations, results of pathogen transmission studies using this An. darlingi colony need to be interpreted cautiously.