A countrywide field survey of immature mosquitoes was conducted in Moldova with the aim to evaluate the Culicidae species composition in different larval habitats and their distribution in the country. In total, 259 potential larval habitats were sampled in the 53 localities, resulting in 9,456 specimens. Twenty species belonging to the genera Anopheles, Aedes, Culex, Culiseta, and Uranotaenia were collected. Mean species richness in aquatic habitats ranged from 1.00 to 4.00, and, for example, was higher in swamps, flood plains, ditches, and large ground pools and lower in rivers, streams, tree-holes, and containers. Six mosquito species were identified only in a single type of aquatic habitat. Anopheles maculipennis s.l., Culex pipiens pipiens L., and Culex modestus Ficalbi were the most abundant and distributed species representing over 80% of the identified specimens. Three, four, and five associated species were recorded from 23.5% of mosquito-positive aquatic habitats. Our findings demonstrate the co-occurrence of Cx. p. pipiens and Culex torrentium Martini in natural and rural environments. It is concluded that the study area has undergone a dramatic ecological change since the previous studies in the 1950s, causing the near extinction of Culex theileri Theobald from Moldova. An. maculipennis s.l. larval abundance, reduced by the DDT control of the adults in the 1950s, had returned to those of the 1940s. Restoration of An. maculipennis s.l. abundance in combination with imported malaria cases constitute a risk of the reintroduction of malaria transmission in Moldova.