AbstractMosquitoes, especiallyAedes aegypti, are becoming important models for studying invasion biology. We characterized genetic variation at 12 microsatellite loci in 79 populations ofAe. aegyptifrom 30 countries in six continents, and used them to infer historical and modern patterns of invasion. Our results support the two subspeciesAe. aegypti formosusandAe. aegypti aegyptias genetically distinct units.Ae. aegypti aegyptipopulations outside Africa are derived from ancestral African populations and are monophyletic. The two subspecies co‐occur in both East Africa (Kenya) and West Africa (Senegal). In rural/forest settings (Rabai District of Kenya), the two subspecies remain genetically distinct, whereas in urban settings, they introgress freely. Populations outside Africa are highly genetically structured likely due to a combination of recent founder effects, discrete discontinuous habitats and low migration rates. Ancestral populations in sub‐Saharan Africa are less genetically structured, as are the populations in Asia. Introduction ofAe. aegyptito the New World coinciding with trans‐Atlantic shipping in the 16th to 18th centuries was followed by its introduction to Asia in the late 19th century from the New World or from now extinct populations in the Mediterranean Basin.Aedes mascarensisis a genetically distinct sister species toAe. aegyptis.l. This study provides a reference database of genetic diversity that can be used to determine the likely origin of new introductions that occur regularly for this invasive species. The genetic uniqueness of many populations and regions has important implications for attempts to controlAe. aegypti, especially for the methods using genetic modification of populations.