Wolbachia is the most common bacterial endosymbiont of arthropods, such as the medically important Aedes albopictus. Recent reports also detected in Aedes aegypti. This study collected 12 adults Ae. albopictus and 359 Ae. aegypti from 183 households in a dengue-prone area, Manila, Philippines, between June and September 2017. Aedes larvae (n = 509) were also collected from 17 water containers from 11 households. The DNA of the Aedes larvae and adults were screened for the presence of Wolbachia using the wsp and 16S markers, following optimized polymerase chain reaction (PCR) conditions, and sequenced. Our results showed that 12 out of 12 (100%) adult Ae. albopictus and3 out of 359 (0.84%) adult Ae. aegypti were Wolbachia positive, whereas all larvae tested negative for Wolbachia (0/509; 0%). The wsp marker revealed six Wolbachia-positive Ae. albopictus belonging to supergroups A (n = 2) and B (n = 4). The 16S marker showed Wolbachia in ten Ae. albopictus and 3 Ae. albipictus,most sequences were in supergroup A (n = 11) and two in supergroup B. Our results revealed Wolbachia supergroups in field-collected Ae. albopictus and Ae. aegypti with implications for a successful Wolbachia mass release programs.