Plant–soil feedback (PSF), regulated by both mycorrhizae and soil pathogens, is a primary mechanism maintaining high tree diversity in the tropics. But how warming may affect PSF is not well understood. We conducted warming experiments on seedling survival of a rhizobia-associated species (Ormosia semicastrata) carrying coevolved host-specific soil-borne pathogens and an ectomycorrhizal fungi-associated species (Cyclobalanopsis patelliormis) immune to soil-borne pathogens. We found elevated temperature lowered seedling mortality of O. semicastrata, but had no detectable effect on C. patelliormis seedlings. This indicates that warming weakened the negative PSF on O. semicastrata but did not affect the positive PSF on C. patelliormis. The differential warming effects on seedling mortality of species with different microbial associations imply that global warming could lead to change in tropical tree composition. Our study also predicts that global warming would undermine the role of the JC effect in maintaining tree species diversity in the tropics.