Phymatotrichopsis omnivora affect a great number of fruit species causing great economic losses and the use of agrochemicals to combat them, resulting in adverse environmental effects, so it would be very useful to find alternatives that contribute to reduce the use of these chemicals. There are soil-borne microorganisms with mechanisms of inhibition towards various pathogens, which contribute to the use of biological control methods. The objective of this work was to select and identify bacteria strains capable of inhibiting the growth of P. omnivora. To do this, bacteria were isolated from roots of fruit trees with the presence of the disease to evaluate their antagonistic effect in vitro. A total of 88 bacterial isolates were obtained, of which the antifungal capacity was evaluated by simultaneous confrontation of the fungus and the bacteria in triplicate assays. Cottonseeds were inoculated with strains that showed significant inhibition, using in vitro cultures. The bacterial strains M1, N8 and N15 presented greater biocontrol capacity and, considering the results obtained, they were identified by 16S ribosomal DNA sequencing.