The microbial communities under different organic crop rhizospheres (0-10 and 10-20 cm) were characterized using fatty acid methyl ester (FAME) and pyrosequencing techniques.  The soil was a silt loam (12.8% clay, 71.8% silt and15.4% sand). Soils at this site are characterized as having pH of ~6.53, and total C of 2.25 g C kg^-1 soil.  Soil samples were taken under lettuce (Lactuca sativa), potato (Solanum Tuberosum), onion (Allium cepa L), broccoli (Brassica oleracea var. botrytis) and Tall fescue pasture grass (Festuca arundinacea). Several FAMEs (a15:0, i15:0, i15:1, i16:0, a17:0, i17:0, i10Me17:0, cy17:0, 16:1ω5c and 18:1ω9c) varied among the crop rhizospheres.  Soil microbial community FAME profiles under pasture showed a significantly higher fungal: bacterial ratio compared to the soil under lettuce, potato, onion, and broccoli. Fungal: bacterial ratios were higher under broccoli and potato compared to onion and lettuce.  Furthermore, microbial biomass C and enzyme activities associated with pasture and potato rhizospheres were higher than the other crop rhizospheres. Another distinct trend found in this study was the lower soil microbial biomass C and enzyme activities under onion compared to all the other crop rhizospheres. Pyrosequencing revealed significant differences on maximum operational taxonomic units (OTU) at 3% dissimilarity level (roughly corresponding to the bacterial species level) at 0-10 cm (581.7- 770.0) compared to 10-20 cm (563.3 -727.7) soil depths, respectively. The lowest OTUs were detected at 0-10 cm under broccoli (581.7); whereas the lowest OTUs were found at 10-20 cm under potato (563.3).  The predominant phyla (85%) in this soil at both depths were Flavobacteria, Sphingobacteria, Proteobacteria and Actinobacteria. Flavobacteriaceae and Xanthomonadaceae were predominant under broccoli. Rhizobiaceae, Hyphomicrobiaceae, and Acidobacteriaceae were more abundant under pasture (grass) compared to the broccoli, potato, onion and lettuce. This study demonstrated the significant differences in microbial communities influenced by each crop rhizosphere in an organic farming system. Differences in microbial community structure and enzyme activities can have implications in soil functioning, processes and soil health, and the yield and nutritional value of each crop.