This study was conducted to characterize larval habitats of Anopheline mosquitoes and to estimate the key ecological factors associated with this group's distribution. The study was carried out during June and July 2009 at 25 localities in 10 sectors of Larache Province. The aquatic habitats were sampled by standard dipping techniques. The habitats were characterized based on water depth, pH, temperature, conductivity, salinity, distance to the nearest house, dissolved oxygen, algae and emergent plants (presence or absence), turbidity and habitat type. A total of 54 aquatic habitats consisting of swamps, rivers and rice fields were chosen. Fifty-two per cent of all habitat samples were positive for Anopheles larvae. Of all mosquito larvae collected, 1145 were Anopheles of which 316 (28 % ) were early instars and 829 (72 % ) late instars. Morphological identification of third and fourth larval instars revealed that 76 % (n = 629) were Anopheles maculipennis s.l. and 24 % (n = 200) were An. cinereus. The only species belonging to the Anopheles maculipennis complex was An. labranchiae. Multiple factorial correspondence analyses (MFCA) showed that the density of An. labranchiae was negatively associated with turbidity, pH and depth in aquatic habitats. These findings suggest that the distribution of An. labranchiae was driven by different environmental factors. This will help in understanding the relationship between habitats, environmental factors and abundance of Anopheles larvae, which is essential for the efficient application of mosquito control methods.