Culex tritaeniorhynchus, Cx. gelidus, and Cx. quinquefasciatus, known vectors of Japanese encephalitis (JE), are distributed in rice agroecosystems in Asian countries. Very few integrated studies on the breeding habitats of rice-field mosquitoes, including JE vectors, have been conducted in Vietnam. We investigated the mosquito fauna and potential predators in 8 rice growing areas in the Mekong Delta region of southern Vietnam, during the wet and dry seasons of 2009. Mosquitoes and their predators were collected from a variety of aquatic habitats (rice fields, ponds, wetlands, shrimp ponds, ditches, canals, and rivers). We collected 936 Culex spp. (354 Cx. tritaeniorhynchus, 240 Cx. vishnui s.l., 189 Cx. fuscocephala, and 42 Cx. gelidus), 33 Uranotaenia, 25 Anopheles, and 9 Mimomyia (4 Mi. chamberlaini) in the dry season. During the rainy season, we collected 1,232 Culex spp. (132 Cx. vishnui s.l., 66 Cx. tritaeniorhynchus, 9 Cx. gelidus, 4 Cx. fuscocephala, and 2 Cx. bitaeniorhynchus), 236 Anopheles spp. (40 An. vagus and 1 An. sinensis), and 7 Uranotaenia (3 Ur. lateralis). Heteroptera such as Micronecta, Veliidae, and Pleidae were abundant and widely distributed in both seasons. Based on a stepwise generalized linear model, the abundance of mosquitoes and their predators in rice fields was high when the rice plant length was short and water depth was shallow. Therefore, the use of insecticides during the earlier stages of rice growth should be avoided in order to preserve the predator populations.