Secondary metabolites synthesized via the polyketide pathway are thought to mediate interference competition between soil microorganisms as well as cell-to-cell signaling. Although their synthesis has been documented in laboratory culture, it remains uncertain whether these compounds are actually produced under field conditions. Here, we report the presence and expression of fungal Type I polyketide synthase (PKS) genes in the organic horizon of a forest soil. If these expressed PKS genes produce compounds that elicit antagonistic interactions among soil microorganisms, then it could be a factor structuring microbial communities in soil.