Aedes aegypti and Culex quinquefasciatus were found in large numbers emerging from septic tanks in southern Puerto Rico during the dry season. Previous studies suggested that Ae. aegypti uses subterranean aquatic habitats only during dry periods when surface containers do not have water. This research investigated whether septic tanks are alternative aquatic habitats that this mosquito uses during unfavorable times of the year, or whether Ae. aegypti uses this aquatic habitat throughout the year. To assess temporal change, exit traps were used to collect mosquitoes emerging from septic tanks in Playa/Playita, southern Puerto Rico, from November 2006 to October 2007. We also investigated the hypotheses that 1) the production of Ae. aegypti in septic tanks was larger than in surface containers and 2) adult mosquitoes emerging from septic tanks were larger than those emerging from surface containers. This study demonstrated that unsealed septic tanks produced large numbers of Ae. aegypti and Cx. quinquefasciatus throughout the year, without any significant relationship with rainfall. The number of adult Ae. aegypti emerging per day from septic tanks in each community was 3 to 9 times larger than those produced in surface containers. It was also demonstrated that Ae. aegypti emerging from septic tanks were significantly larger than those emerging from surface container habitats. It is recommended that dengue prevention programs include regular inspection and maintenance of septic tanks in communities lacking sewerage.