This study aimed to analyze the resistance of the thermally treated wood of Pinus caribaea and Eucalyptus saligna to the biological attack of wood rotting fungi. The heat treatment processes were carried out in electric oven under nitrogen atmosphere, starting from 100 °C until reaching each one of the final temperatures of the process: 120, 140, 160, and 180 °C. The resistance assays were performed for white rot, brown rot, and soft rot fungi. The increase in decay resistance was observed for heat-treated wood of Pinus caribaea at higher temperatures. On the other hand, Eucalyptus saligna showed increased resistance to rotting fungi at all tested temperatures, except for white and soft rot at 120 °C. In general, the heat treatment process showed good results for its use as a wood preservative method.