Agricultural practices affect soil microbial communities and soil health through the input of pesticides, herbicides, and fertilizers. By examining the microbial community structures, we can learn how different microbial species respond to the environment that organic and conventional farming practices create. A comparative study of organic and conventional tomato production systems was conducted by analysis of soil collected from two conventional and two organic farms in Southeast Georgia. Molecular methods including length heterogeneity polymerase chain reaction (LH-PCR), quantitative PCR (QPCR), cloning, and sequencing were applied to analyze soil fungal, bacterial, and animal communities. The LH-PCR fragment analysis of the fungal, bacterial, and animal DNA followed by cluster analysis indicated that the fungal and bacterial communities are unique to the management practice conducted. Bacterial and fungal communities shared ~45% and ~40% similarity respectively for organic management practices, but only ~20% similarity for conventional management practices. The animal communities were not clearly separated, and did not show distinction between organic and conventional management practices. Analysis of Similarity (ANOSIM) showed that each community for bacteria, fungi, and animal was different overall (P=0.008) under conventional and organic management practices. Pairwise tests indicated that the bacterial and fungal communities of each farm were significantly different (P=0.008), but showed a mix of differences for the animal communities. Biotic/abiotic analysis suggested that changed soil abiotic characteristics through organic agricultural practices greatly affected soil fungal and bacterial community structure and may further contribute to soil-borne disease incidence in tomato production.  The chemical components of the soil samples under organic and conventional management practices were significantly different (MANOVA, P<0.0001), including percentage of organic matter (P<0.0001), potassium PPM (P=0.0045), magnesium PPM (P<0.0001), soil pH (P<0.0001), nitrate PPM (P=0.0055), K% base saturation (P<0.0001), and Mg% base saturation (P=0.0001).