The coffee berry borer (CBB), Hypothenemus hampei, is considered the most important insect pest of coffee worldwide. CBB was discovered on Hawai'i Island in 2010 and soon thereafter on the islands of O'ahu (2014) and Maui (2016). As part of an areawide effort to manage CBB in Hawai'i, we conducted a survey of naturally-occurring Beauveria associated with the beetle to complement field efficacy studies of the commercial B. bassiana strain GHA. Sampling of CBB from coffee farms or unmanaged sites in various districts on the islands of Hawai'i and O'ahu, and also from Puerto Rico, resulted in >1800 Beauveria isolates. These were initially characterized using colony morphology to differentiate strain GHA, registered for use in Hawai'i, from indigenous congenerics. A total of 114 isolates representative of these indigenous morphotypes were selected for further characterization. Sequencing of the intergenic regions B locus and EFutr identified all as Beauveria bassiana sensu stricto. Sixteen haplotypes were observed, with one more common haplotype present in 12 of 16 sites sampled on Hawai'i Island. This B locus-EFutr haplotype, designated Bb1, was the only haplotype observed in 2016 epizootics on two high-elevation coffee farms on Hawai'i Island with no history of GHA application. Many of the haplotypes showed genetic similarity to those collected from CBB from other countries, including Brazil, Columbia, Nicaragua, and Kenya, but a few were identical to those from other insect species collected in Hawai'i before 2010. This diversity suggests a mixed lineage among B. bassiana strains associated with CBB in the three Hawaiian islands.