Aedes aegypti (Linnaeus, 1762) is the mosquito species responsible for transmission of yellow and dengue fevers. Different strategies are used worldwide to reduce its abundance, but effectiveness is not well understood. The aim of this work was to evaluate the effectiveness of chemical control of larvae of this species using different indices before and after application at three locations in Baja California Sur, Mexico. The presence of Ae. aegypti larvae was evaluated by three larval indices: house index, container index, and Breteau index at three locations at Cabo San Lucas, La Paz, and San Jose del Cabo during 3 years (2011–2013) before and after chemical control and reduction of potential breeding sites by the Secretaria de Salud (health department of Baja California Sur). The data showed significant statistical differences (p < 0.001) in the relative abundance of Ae. aegypti larvae before and after applying larvicide (Temephos®) and by removing water containers where mosquitoes reproduce, regardless of the type of index used for the analysis. In La Paz, the average of the housing index was reduced from 16–83% to 0–5% after control during the 3 years. In Cabo San Lucas, the value was reduced from 2–40% to <1% and in San Jose del Cabo such variation was 4–46% to 0–7%. The index of positive containers before and after management varied in La Paz from 6–34% to 0–4.7%; in Cabo San Lucas from 0.2–23% to <1%, and in San Jose del Cabo from 0.6–11% to <1.2%. The Breteau index in La Paz varied from 48–358% to 0–12.5%, in Cabo San Lucas, values decreased from 3–67% to <1%, and in San Jose del Cabo from 3–174% to 0–16% after vector-control measures were applied. Our data suggested that controls applied in Baja California Sur on Ae. aegypti larvae were effective enough to reduce the relative abundance of larvae of the species. However, other strategies are necessary to ensure elimination of Ae. aegypti larvae homes, thereby reducing impact on human health in the zone.