BACKGROUND A previous phylogeographic study revealed two Aedes aegypti African-related mitochondrial lineages distributed in Colombian's cities with different eco-epidemiologic characteristics with regard to dengue virus (DENV). It has been proposed these lineages might indicate independent invasion sources. OBJECTIVES Assessing to Colombian population structure and to support evidence of its probable source origin. METHODS We analysed a total of 267 individuals from cities of Bello, Riohacha and Villavicencio, which 241 were related to the West and East African mitochondrial lineages (termed here as WAL and EAL, respectively). Eight polymorphic microsatellite loci were analysed aiming population structure. FINDINGS Results indicate substantial gene flow among distant and low-connected cities composing a panmictic population with incipient local differentiation of Ae. aegypti is placed in Colombia. Likewise, genetic evidence indicates no significant differences among individuals related to WAL and EAL is placed. MAIN CONCLUSIONS Minimal genetic differentiation in low-connected Ae. aegypti populations of Colombia, and lack concordance between mitochondrial and nuclear genealogies suggest that Colombian Ae. aegypti shared a common demographic history. Under this scenario, we suggest current Ae. aegypti population structure reflects a single origin instead of contemporary migration, which founding populations have a single source from a mitochondrial polymorphic African ancient.