The effect of natural-occurring salts, boron, and selenium on soil microbial community composition associated with plant survival is not known until recently. This information is needed as soil microorganisms may play a vital role in sustaining health of soil and or tolerance of plants grown in such poor quality soils by contributing to nutrient cycling, soil structure, and overall soil quality and plant survival. Soil microbial communities were compared under poplar trees (Populus spp.) grown in highly contaminated clay-like soils of the west side of California, as well as non-contaminated sandy loam soils from the USDA-ARS San Joaquin Valley Agricultural Sciences Center, Parlier, CA. Phospholipid fatty acid (PLFA) analysis was used to characterize soil microbial community structure for trees grown at both locations. The primary objective of this study is to examine and compare the microbial community structure and biomass in contaminated, as well as uncontaminated soils under poplar trees. Effects of soil salt, boron, and selenium on gram positive bacteria, gram negative bacteria, actinomycetes, fungi, arbuscular mycorrhizal fungi, and protozoa will be discussed to better understand their potential impact on salt and boron tolerance of selected poplar clones.