Zaprionus indianus (fig fly) is a drosophilid of African origin that was recorded in Brazilian territory in 1999, quickly dispersing throughout the country, causing impacts on fig culture, and becoming one of the dominant Drosophilidae species in the Cerrado biome. Due to the fact it is an invasive species and a potential pest in fruit cultivars, it is essential to monitor the variations in the populations of this species aiming to verify its genetic and demographic structure and possible impacts on the drosophilid community. The demography and the genetic data obtained from the Est3 polymorphism of fig fly have been evaluated in six populations of Brazilian Cerrado sampled during the dry season. Multivariate analyses of PCA, UPGMA and landscape genetics were performed. The results have indicated variation in the demography of the sampled populations, the presence of two alleles (Est31 and Est34) in all of them, and a higher isolation degree of the Guaíra (SP) population. Thus, the fig fly is a colonizer of the Brazilian Cerrado, and the polymorphisms of Est3 locus are an appropriate genetic marker to investigate the bioinvasion process.