The analysis of soil microbial communities has relied on culturing techniques using a variety of culture media designed to maximize the recovery of diverse microbial populations. However, only a small fraction (0.1%) of the soil microbial community has been accessible with this approach. In this study we have used phospholipid fatty acids and DGGE profiles to access a greater proportion of the soil bacterial community in order to understand the phylogenetic diversity existing in three acid soils. Results suggested that no direct relationships existed between bacterial community structure, soil enzyme activities and soil nutrient status. The Shannon index was significantly highest in Kodaiakanal acid soil (2.48) than that in other two acid soil. The Dice coefficient was the highest between Kodaikanal acidic and Manipur acidic soil representing a great amount of similarity between them. Total PLFA (mole %), was found to be highest in Kodaikanal acid soil (76.09 %), followed by Uttarakhand acid soil (70.91%). Principal component analysis (PCA) analysis clearly indicated site dependent differences in the bacterial community of the three soils.