In the tropics the contribution of bees as pollinators of important economic indigenous crops remains largely undocumented. We studied the diversity of bee species visiting indigenous tomato (Solanum lycopersicon) and habanero pepper (Capsicum chinense) in subtropical Yucatán, México. The contribution of two native bees, Exomalopsis (E) and Augochloropsis (AG) was compared with that of the introduced Africanized Apis mellífera (HB) for pollinating unvisited flowers in both crops. Apis mellífera and stingless bees were dominant in habanero pepper but solitary bee species were important visitors of tomato. In spite of both crops being autogamic, there was a significant contribution of native bees for pollination of both tomato and habanero pepper. The comparison of fruit weight, number of seeds, and a pollination index based on the latter showed that E and AG were more effective pollinators compared to HB in both crops (ca. Spear’s index of ca. 0.7 vs. 0.35 respectively). In tomato, a further evaluation of the contribution to pollination provided by the three bee species was made using the rate of visits to flowers. Although E and AG were the most efficient pollinators at single flower visits in tomato, none of the three species (including HB) were able to provide single visits to all flowers per unit time to the crop. Our results underline the importance of maintaining diverse assemblages and abundant populations of bee species that can synergically contribute to the productivity of tomato and hot pepper in the Neotropics.