With more than 633 species, Apanteles is the largest genus within the subfamily Microgastrinae (Hymenoptera, Braconidae). We describe three new species reared from pests of commercial fruits, Apanteles ahuacatl Shimbori, Giacomelli & Fernández-Triana sp. n., A. aratiku Shimbori sp. n., and A. mayochinchipe Shimbori sp. n. They parasitize caterpillars in the subfamily Stenomatinae (Depressariidae): the soursop moth Cerconota anonella (Sepp), in fruits of sweetsop (Annona squamosa L.) and atemoya (Annona squamosa x Annona cherimola Mill.) (Annonaceae), the avocado borer Stenoma catenifer Walsingham, in fruits of avocado (Persea americana Mill.) (Lauraceae), and the cacao shoot borer Stenoma decora Zeller, in fruits and shoots of cacao (Theobroma cacao L.) (Malvaceae). The new Apanteles species are included in an expanded version of the key provided by Fernández-Triana et al. (2014) for the Apanteles adelinamoralesae species group. In addition, the previous record of Apanteles stenomae Muesebeck in Brazil is revised and considered to actually represent the species A. yolandarojasae Fernández-Triana.