Dengue is a highly endemic disease in Southeast Asia and is transmitted primarily by the mosquito, Aedes aegypti. The National Capital Region (NCR) of the Philippines, or Metropolitan Manila, is a highly urbanized area that is greatly affected by this arboviral disease. Urbanization has been shown to increase the dispersal of this mosquito vector. For this reason, we conducted a fine-scale population genetic study of Ae. aegypti in this region. We collected adult Ae. aegypti mosquitoes (n = 526 individuals) within the region (n = 21 study areas) and characterized the present population structure and the genetic relatedness among mosquito populations. We genotyped 11 microsatellite loci from all sampled mosquito individuals and analyzed their genetic diversity, differentiation and structure. The results revealed low genetic differentiation across mosquito populations which suggest high gene flow and/or weak genetic drift among mosquito populations. Bayesian analysis indicated multiple genetic structures (K = 3–6), with no clear genetically distinct population structures. This result implies the passive or long-distance dispersal capability nature Ae. aegypti possibly through human-mediated transportation. The constructed dendrogram in this study describes the potential passive dispersal patterns across Metropolitan Manila. Furthermore, spatial autocorrelation analysis showed the limited and active dispersal capability (<1km) of the mosquito vector. Our findings are consistent with previous studies that investigated the genetic structure and dual (active and passive) dispersal capability of Ae. aegypti in a fine-scale highly urbanized area.