Risk assessment studies of field releases of a microbial control agent typically focus on beneficial organisms that may serve as an alternate host of the pathogen. Little is known about the effects of microbial agents on indigenous conspecific strains in agricultural fields. In this study we are evaluating the effects of mass releases of a commercial formulation of Beauveria bassiana strain GHA on naturally occurring conspecific strains by comparing prevalence of, and genetic diversity within, indigenous populations of B. bassiana in fields with no history of GHA treatment and in fields representing a range of GHA application histories. Genetic diversity in B. bassiana isolates collected from soil core samples from four potato farms in Maine and two in New York, representing different treatments, was examined using amplified fragment-length polymorphisms and random amplified polymorphic DNA markers. Our data show greater diversity among populations in untreated fields than in GHA-treated fields, with displacement of indigenous strains in treated fields by GHA or GHA-similar haplotypes. This displacement, however, appears to be temporary with recovery of native strains over time since the last GHA application. The potential for recombination between GHA and indigenous strains, which could result in novel haplotypes, is also being investigated by determining vegetative compatibility groups among the more predominant native strains and GHA.