Isolations of Trichoderma spp. and Bacillus spp. with high antagonistic potential to control Phymatotrichopsis omnivora, a soil pathogen responsible of root rot in several species well know as texas root rot, were realized. The aim of this study was to select and identify to a specie level, native strains collected in northern Mexico that allow them to control efficiently Phymatotrichopsis omnivora. Three Trichoderma isolates were selected for their antagonistic capacity and behavior in vitro against P. omnivora. Molecular identification of the isolates showed (TB = isolated bugambilia; TM = isolated mango; TF = isolated ficus) and the control strain (TN = isolated nogal) the following results: TB and TM strains corresponded to asperellum species and strains TF and TN to virens species. The three strains tested showed high antagonistic potential when compared to the control strain (TN) and will be considered in subsequent evaluations in greenhouses. All strains showed Classes 1 and 2 of antagonism against the pathogen (values from 1,0 to 1,5), according to the scale of Baker & Cook. At the same time, 32 isolates of Bacillus spp. were obtained and four were selected because of their greater zone of inhibition against Phymatotrichopsis omnivora (B6 = isolated jatropha; B14 = isolated mango; B18 = isolated corn; B21 = isolated corn). The results of the molecular identification of the isolates were directed to B6, B14 and B18 strains belong to the species cereus sensu lato, while the B21 strain to the species subtillis. These results contribute to biological control against Phymatotrichopsis omnivora that affects a great number of plants.