The black salt-marsh mosquito, Aedes taeniorhynchus, plays an important role in the transmission of arboviruses such as West Nile virus and other pathogens of concern for human and animal health in North and Latin America. This mosquito is notably the only widely distributed mosquito species found in the Galápagos Islands, where its impact as disease vector has not yet been studied. The use of microsatellite markers can significantly improve our understanding of the population structure and dynamics of A. taeniorhynchus and its role in the transmission of diseases. Here we report the isolation of 12 unique microsatellite loci using an enrichment protocol. We also identified other multi-locus microsatellites linked to transposable elements. The presence of such elements may explain why the isolation of useful scorable microsatellite markers in the Aedes genus is often difficult. Four of the markers isolated amplified polymorphic products in Aedes aegypti, Aedes albopictus and/or Aedes japonicus.