This is the first complete inventory of stingless bees in El Salvador. It includes the spatial distribution of wild and managed colonies and the relationships between their occurrence and vegetation cover, altitude and temperature. Applying a stratified sampling, we located wild colonies (n = 477) and managed colonies (n = 686) of stingless bees in tropical forests, agricultural fields and urban areas. Each stratum (14) was a department (political division) of El Salvador. We made maps of the distribution of the most common wild and managed species. We analysed spatial distribution of colonies through the Clark and Evans Index (CEI). For the estimation of diversity between departments, the Shannon-Wiener diversity index (H) was calculated. The relationship between species richness and vegetation cover was analysed through the chi-square test. Linear regression was used to evaluate the effects of altitude and temperature on species richness. We concluded that: (a) there are at least 20 species, six subgenera and 10 genera of stingless bees in El Salvador; (b) the departments with highest levels of diversity were Santa Ana (H′ = 2.55), Chalatenango (H′ = 2.41), Morazán (H′ = 2.31) and La Libertad (H′ = 2.22); (c) the most abundant wild species, was Tetragonisca angustula (n = 156, relative abundance = 32.70%) and was found in each department in clustered pattern (CEI = .26, p < .001); (d) Melipona beecheii (n = 405, relative abundance = 59.04%) was the most frequent managed species, mainly found in a clustered pattern (CEI = .28, p < .001) in the northern and the western part of El Salvador; (e) the species richness is associated with the vegetation cover: increased with coniferous forest (X2 = 336.1, p < .001), fruit trees (X2 = 41.8, p < .001), and with temperature (r = .86, p = .0015) but decreased with altitude (r = −.87, p = .001).