Rhizosphere-associated microbiota can contribute to functioning of agroecosystems. The insect-pathogenic fungus Metarhizium is an important component of this microbiota and can contribute to the suppression of insect pests, potentially reducing the need for agricultural inputs. We examine the species composition of Metarhizium in a coffee agroecosystem, sampling isolates from rhizosphere and associated soils of five groups of plants. Coffee, trees and spontaneous monocotyledons harboured the greatest density of Metarhizium and species. Five Metarhizium species were revealed by 5'TEF DNA sequences, being M. robertsii isolated in all the groups of plants and soil. Considering its high prevalence, it may be important in strengthening interactions between soilborne fungi and natural enemies of pests within agroforests. Metarhizium pemphigi was the second most abundant species and was isolated mostly from coffee roots, indicating a potential ecological specialization of this fungus colonising coffee plants. We observed a great abundance and diversity of Metarhizium in plant roots, suggesting that a diversified agroecological system may foster this diversity and benefit from these fungi playing varied roles in the rhizosphere and soil. In particular, native M. pemphigi could be investigated as an inoculant in coffee as it appears to be capable of establishing persistent associations with the plant.