The effects of chlorothalonil (CTN), butylated hydroxytoluene (BHT), and ammoniacal copper quat (ACQ-C) on the fungal community on southern yellow pine (SYP) were assessed using terminal restriction fragment length polymorphism (T-RFLP) analysis over 15 months. Field stakes, treated with 0.25 and 0.37% ACQ-C, 0.1 and 0.25% CTN, 2% BHT alone, 0.1 and 0.25% CTN combined with 2% BHT, and untreated controls, were installed in two field sites in Mississippi. Stakes were sampled at 90-day intervals and rated for decay damage. Fungal DNA was extracted and amplified by non-specific (total fungi) and specific (Basidiomycete) primers and processes for T-RFLP. a-Diversity (richness and diversity) and b-diversity (similarity between communities) were calculated by means of T-RFLP data. The presence of wood preservatives slowed the initial colonization of field stakes by total fungi, resulting in lower richness and diversity that increased over time; however, preservatives increased the richness and diversity of Basidiomycetes. The b-diversity of treated samples was less similar in the early stages of exposure (3–9 months), but coalesced over time into equilibrium communities that were similar to communities on untreated controls. Basidiomycete species compositions were different among treated samples while control communities shared more than 75% of their species. Correlations were found between depletion of 0.1% CTN and increasing fungal diversity, but no other significant correlations were found.