Chagas disease is a serious public health problem in Ecuador, where nearly 230,000 individuals show Trypanosoma cruzi infection. Sylvatic T. cruzi transmission is a threat to current control strategies. This is because of the possibility of house reinfestation by sylvatic triatomines after insecticide treatment. This work quantified the spatial distribution of triatomines in sylvatic habitats and its relationship with nearby human dwellings. A simple random sampling design using live-baited traps and manual searches for triatomines was used in areas near human communities in Manabí province, Ecuador, during June and July 2007. We identified risk factors associated with triatomine density using generalized linear models, and developed predictive maps for triatomine density interpolation. There were 345 triatomines belonging to the species Rhodnius ecuadoriensis and Panstrongylus howardi collected in sylvatic areas. Spatial analyses revealed an aggregated distribution pattern of the sylvatic triatomine populations (clustered mostly at a distance smaller than 100 m). Generalized linear models showed that the distance from the nearest house, nest type, and height from ground level were the main factors explaining triatomine densities. Squirrel nests (Sciurus stramineus), located in plants other than palms, above 5 m and close to the domicile presented higher infestation. Interpolation maps of triatomine microdistribution are presented as potential tools to predict triatomine occurrence. The presence of sylvatic populations and the synanthropic tendency of the vectors highlight the need for continuous active and passive entomological surveillance for the long-term control of Chagas disease.