As part of a project aimed at developing a biological control program against the coffee berry borer, we have sampled fungal endophytes in Hawaii, Colombia, Puerto Rico and Mexico. The objective was to determine what constraints might be faced in the field by the fungal entomopathogen Beauveria bassiana, which we were able to establish as a fungal endophyte in coffee in laboratory tests. Over 700 fungal endophyte isolates were sequenced: 281 from Colombia, 240 from Hawaii, 119 from Mexico, and 68 from Puerto Rico. These comprise more than 170 distinct unique sequences. The most common genera were Colletotrichum, Fusarium, Penicillium, and Xylaria. We also isolated five genera of fungal entomopathogens (Acremonium, Beauveria, Cladosporium, Clonostachys, and Paecilomyces) and eleven known Penicillium species, four of which produced ochratoxin. We have also discovered fungal and bacterial endophytes in green coffee seeds. The role of endophytes in coffee tissues remains enigmatic and deserves further study.