Malaria incidence has recently decreased globally and, as malaria elimination is envisioned as a possibility by the health authorities, guidance is needed to strengthen malaria control strategies. Larval source treatment, which could complement routine vector control strategies, requires knowledge regarding the Anopheles larval habitats. A cross-sectional study was conducted in three of the most malaria-endemic regions in Colombia. A total of 1116 potential larval habitats in 70 villages were sampled in three states located in western Colombia: Cordoba, Valle del Cauca and Nariño. Overall, 17.5 % (195) of the potential larval habitats were found positive for different Anopheles species. A total of 1683 larvae were identified belonging to seven species: Anopheles albimanus, Anopheles calderoni, Anopheles darlingi, Anopheles neomaculipalpus, Anopheles nuneztovari s.l., Anopheles pseudopunctipennis, and Anopheles triannulatus. The most widely distributed species was An. nuneztovari s.l., which was found mainly in human-made fishponds in Cordoba and temporary puddles in Valle del Cauca. Anopheles albimanus and An. calderoni were associated with human-made wells or excavation sites in Nariño. Cordoba displayed the greatest Anopheles species diversity with a total of six species (Shannon diversity index H′: 1.063). Although Valle del Cauca had four species, one more than Nariño, the diversity was lower because only one species predominated, An. nuneztovari s.l. The larval habitats with the highest Shannon diversity index were lagoons (H′: 1.079) and fishponds (H′: 1.009) in Cordoba, excavation sites in Nariño (H′: 0.620) and puddles in Valle del Cauca (H′: 0.764). This study provides important information regarding the larval habitats of the main malaria vectors in the most malaria-endemic regions of Colombia, which will be useful in guiding larval control operations.