Insect vector–borne diseases continue to present a major challenge to human health. Understanding the factors that regulate the size of mosquito populations is considered fundamental to the ability to predict disease transmission rates and for vector population control. The mosquito, Anopheles pseudopunctipennis, a vector of Plasmodium spp., breeds in riverside pools containing filamentous algae in Mesoamerica. Breeding pools along 3 km sections of the River Coatán, Chiapas, Mexico were subjected to algal extraction or left as controls in a cross-over trial extending over 2 years. Initial densities of An. pseudopunctipennis larvae were directly proportional to the prevalence of filamentous algae in each breeding site. The extraction of algae brought about a striking decline in the density of An. pseudopunctipennis larvae sustained for about six weeks, and a concurrent reduction in the adult population in both years of the study. Mark–release experiments indicated that dispersal from adjacent untreated areas was unlikely to exert an important influence on the magnitude of mosquito control that we observed. Habitat manipulation by extraction of filamentous algae offers a unique opportunity for sustainable control of this malaria vector. This technique may represent a valuable intervention, complimenting insecticide spraying of households, to minimize Plasmodium transmission rates in Mesoamerica.