The establishment and spread of genes introduced into mosquito populations is contingent upon their movement among individuals via mating. Patterns of gene flow can be ascertained directly by examining individuals to describe mating patterns or by describing differences in the frequency of naturally occurring and selectively neutral genetic markers among populations. The genetics of Anopheles gambiae populations is complex. The genetic structure of populations varies from place to place and even seasonally and some factors that affect levels of gene flow have been identified. Geological features have been demonstrated to act as barriers to gene flow between populations in east Africa and the movement of genes between mainland and island populations appear to be restricted. Sympatric sub-populations, distinguishable by genetic markers, appear to be isolated by assortative mating. However, the strength of pre-mating reproductive barriers, differ from place to place. Populations differing with respect to the combinations of paracentric inversions they possess have non-random spatial and temporal distributions and these appear to be impacted by local or seasonal differences in rainfall levels. In this presentation the literature describing An. gambiae population genetics will be critically reviewed and discussed. Inconsistencies among different reports will be analyzed with respect to the types of genetic markers employed and their limitations and to what extent these are the consequence of real differences in the biology of this species over it’s range. Finally, how this knowledge relates to the application of genetically modified mosquitoes for the control of malaria in Africa will be discussed.