Existing ponderosa pine forests often contain stands of small diameter, high density trees, a closed-canopy structure, significant forest floor biomass, and little herbaceous understory. These stands present conditions that are ripe for catastrophic crown fires, especially when located adjacent to urban areas. Current fuel reduction programs at the wildland/urban interfaces often involve thinning. To date there is little information on the soil microbial community structure of these stands or how they will be affected by thinning. In the early 1960's a project was initiated to determine appropriate stocking levels of ponderosa pine at several western locations. Stocking levels at these stands have been maintained for over forty years. We sampled three different stocking levels at each location in the summer of 2003 (dry period) and 2005 (wet period), to assess long-term affects on the soil microbial communities. Moisture conditions during the growing season and location were the major influences on soil microbial community structure while stocking level was not a significant determinant.