Fusarium circinatum Nirenberg & O’Donnell, the pitch canker fungus, has been recently reported in Uruguay affecting Pinus taeda L. seedlings. The spread of this pathogen to plantations constitute a risk to forestry production. The aim of this work was to evaluate the inhibitory effect of live bacteria and their thermostable metabolites on F. circinatum growth in vitro. Four Bacillus subtilis strains and one of Burkholderia sp. isolated as P. taeda endophytes were evaluated as biological control agents of F. circinatum. Dual cultures between live bacteria and pathogen were performed. Furthermore, bacteria metabolites obtained from liquid cultures were sterilized and added to the culture media where fungus was grown. In this study all bacteria showed an antagonist effect on the pathogen growth arresting the mycelia at one cm of the edge of the bacteria colony. Bacteria thermostable metabolites reduced over 50% fungal growth. These results demonstrates that endophytic bacteria, well adapted to live in host tissues, constitute a good alternative to control F. circinatum affecting Pinus seedlings.