Abstract : We have used sequencing of targeted 16S rDNA PCR libraries and random metagenomic libraries to examine the phylogenetic and genomic diversity within the human gastrointestinal bacterial community. In one study, we used both 16S and metagenomic analysis in a study of fecal samples from three healthy human subjects. In a second study, we used 16S analysis to compare bacterial diversity between samples obtained from multiple intestinal mucosal sites and companion fecal samples of multiple healthy individuals. These studies demonstrate a remarkable diversity between bacterial communities in the different sites within the gastrointestinal tract and also between individuals. Through the metagenomic approach, we have identified genome sequences from fungal and archael organisms and identified several virulence genes as potential markers of pathogens within the population. Finally, we have modified our DNA assembly program, Celera Assembler, to successfully assemble contigs up to ^40 kb from the random metagenomic sequence data.