Despite the increasing interest in studying Cladocera and Copepoda in Philippine freshwaters, there is a need to update our knowledge on its taxonomy and distribution in highly urbanized areas, such as Metropolitan Manila. This paper presents an updated listing of freshwater microcrustaceans and their distribution in Metropolitan Manila, considering the continued deterioration of water quality and increased urbanization in many areas since the last comprehensive study on these taxa in 1950s. We collected water samples from 33 freshwater sites in Metropolitan Manila and 23 of which were found to contain microcrustacean zooplankton. A total of 13 species were identified including two new locality records for C. cornuta and D. dubium in Pasig River. All 8 cladocerans, we identified have already recorded in previous studies while 3 cyclopoid copepods are new records for Metropolitan Manila. Furthermore, 16% of all known freshwater microcrustacean zooplankton species in the Philippines are found in Metropolitan Manila, including the Luzon-endemic Filipinodiaptomus insulanus collected from man-made reservoirs in less-disturbed habitats (an urban wildlife park, golf course and eco-park). Other identified species such as Thermocyclops taihokuensis may serve as indicator for high levels of nutrient. These results point to the importance of monitoring urban aquatic biodiversity for their potential in determining aquatic ecosystem health and of maintaining urban aquatic sanctuaries which may serve as alternative habitat for flora and fauna in rapidly developing urban centers such as Metropolitan Manila.