Technical Abstract: This is the first known pyrosequencing assessment of plant-endophyes residing within roots. The assessment suggests that the microbial assemblage residing within plant tissues is cultivar-specific and its phylotype richness is several orders of magnitude greater than previously believed. This new pyrosequencing method application can serve to reveal bacterial diversity in plant roots not detectable by other methods, which could bring a number of unanticipated benefits, ranging from more accurate microflora diversity assessment and quantification, to supporting further studies that examine the contribution of microflora on plant physiology, production, soil health, and environmental conservation.