The present study was conducted to evaluate the application of native phosphate solubilizing Bacillus sp., isolated from Prosopis juliflora rhizosphere in the biocontrol of three different Fusarium species. The native Bacillus sp., was further confirmed as B. subtilis using the Polymerase Chain Reaction (PCR). The results showed that the phosphate solubilizing ability of B. subtilis strain ALICA was tested in liquid medium with 0.5% Ca3(PO4)2, and maximum of the value of soluble phosphate was 202.02 µg/mL after 3 days of incubation. On the other hand, the growth inhibition of Fusarium solani, F. equiseti and F. oxysporum were more evident in cell-free medium filtrates with respect to dual medium with a range of percentage inhibition from 51, 66 and 47% after 5 days, respectively. Our result of the DNA-PCR amplification of the lipopeptide genes from B. subtilis strain ALICA, showed 94% identity with subtilosin and subtilisin of different Bacillus spp. This result turns B. subtilis strain ALICA into a potential alternative for the biological control of Fusarium species present in the soil of transgenic insect-resistant cotton plants in Mexico.