Management induced microbial community shifts may be linked to soil organic matter stability. The objective of our study is to elucidate how microbial composition shifts with different agricultural practices. Soil samples (0-20 cm depth) were collected from Hoytville, Ohio.  Experimental treatments included native forest (NF), conventional tillage maize (CT) and no tillage maize (NT). Partial ribosomal amplification on extracted DNA with tag encoded primers and 454 FLX titanium pyrosequencing were used to estimate microbial diversity and community composition. After quality trimming, 62639 bacterial and 413,940 fungal sequences were clustered at 97% similarity into 7171 and 4605 OTUs, respectively. Rarefaction curves of OTU diversity kept increasing for bacteria at 2400 OTUs but leveled off at ~600 OTUs for fungi. There were no significant differences in species diversity (Simpson and Shannon indices) and OTU richness among treatments. Relative abundance of Proteobacteria, Bacteroidetes, Actinobacteria and Firmicutes was higher in disturbed systems than forest, in contrast to Acidobacteria and Verrucomicrobia. Redundancy analysis showed 65% of the variation in bacterial communities (p=0.015) and 40% of variation in fungal communities (p=0.01) was explained by treatments. This study demonstrated that the soil microbial community structure shifts with implementation of different agricultural practices known to influence the amount of carbon stored in soil. Further studies are determining carbon pool size and flux on these sites and how treatments affect microbial community composition at different stages of decomposition over long periods of time.