Abstract Increased DEN-2 virus transmission in Puerto Rico during 2005 prompted the implementation of a rapid intervention programme to suppress Aedes aegypti (L.) (Diptera: Culicidae) emergence, which in turn lead to the discovery of previously unknown breeding sites underground. Initially, the following control measures were applied in Playa/Playita (PP), a town of 1,400 households, to all areas where the number of pupae per person exceeded the expected threshold for dengue transmission; all containers likely to be aquatic habitats were turned over and containers too large to turn were treated with 1 p.p.m. methoprene. The impact of these interventions was evaluated by comparing the number of resting adult mosquitoes (by backpack aspiration and sweepnetting in bedrooms) pre-intervention, with numbers at 3 and 5 weeks post-intervention, and by evaluating pupal density at 4 weeks post-intervention in PP and in a nearby town, Coqui (CO; 1500 households), which was not treated. The pre-intervention and post-intervention densities of resting Ae. aegypti adults were significantly larger in the intervention town, although the density of pupae in surface containers was low and similar in both towns at 4 weeks post-intervention. At 3 weeks post-intervention, the density of resting adults decreased by only 18% of pre-intervention levels, but returned to pre-intervention levels 5 weeks after treatment. By contrast, the density of resting adults in CO steadily decreased to 48% and 61%, at 3 and 5 weeks after the initial surveys, respectively. Geographical Information Systems identified significant clustering of adult mosquitoes, which led to the discovery of underground aquatic habitats (septic tanks) that were producing large numbers of Ae. aegypti and Culex quinquefasciatus (Say) in the treated town. We calculated that septic tanks could produce > 18 000 Ae. aegypti and ~ 170 000 Cx quinquefasciatus adults per day. Septic tanks are likely to be common and widespread in suburban and rural Puerto Rico, where, apparently, they can contribute significantly to the maintenance of island-wide dengue virus endemicity.