Background Aedes aegypti is a vector of several arboviruses, notably dengue virus (DENV), which causes dengue fever and is often found resting indoors. Culex spp. are largely nuisance mosquitoes but can include species that are vectors of zoonotic pathogens. Vector control is currently the main method to control dengue outbreaks. Indoor residual spraying can be part of an effective vector control strategy but requires an understanding of the resting behavior. Here we focus on the indoor-resting behavior of Ae. aegypti and Culex spp. in northeastern Thailand. Methods Mosquitoes were collected in 240 houses in rural and urban settings from May to August 2019 at two collection times (morning/afternoon), in four room types (bedroom, bathroom, living room and kitchen) in each house and at three wall heights (< 0.75 m, 0.75–1.5 m, > 1.5 m) using a battery-driven aspirator and sticky traps. Household characteristics were ascertained. Mosquitoes were identified as Ae. aegypti, Aedes albopictus and Culex spp. Dengue virus was detected in Ae. aegypti. Association analyses between urban/rural and within-house location (wall height, room), household variables, geckos and mosquito abundance were performed. Results A total of 2874 mosquitoes were collected using aspirators and 1830 using sticky traps. Aedes aegypti and Culex spp. accounted for 44.78% and 53.17% of the specimens, respectively. Only 2.05% were Ae. albopictus. Aedes aegypti and Culex spp. rested most abundantly at intermediate and low heights in bedrooms or bathrooms (96.6% and 85.2% for each taxon of the total, respectively). Clothes hanging at intermediate heights were associated with higher mean numbers of Ae. aegypti in rural settings (0.81 [SEM: 0.08] vs. low: 0.61 [0.08] and high: 0.32 [0.09]). Use of larval control was associated with lower numbers of Ae. aegypti (yes: 0.61 [0.08]; no: 0.70 [0.07]). All DENV-positive Ae. aegypti (1.7%, 5 of 422) were collected in the rural areas and included specimens with single, double and even triple serotype infections. Conclusions Knowledge of the indoor resting behavior of adult mosquitoes and associated environmental factors can guide the choice of the most appropriate and effective vector control method. Our work suggests that vector control using targeted indoor residual spraying and/or potentially spatial repellents focusing on walls at heights lower than 1.5 m in bedrooms and bathrooms could be part of an integrated effective strategy for dengue vector control.