Due to analytical limitations, patterns of richness and evenness of microbes are scarce in the current literature. The newest and powerful pyrosequencing technology may solve this issue by sampling thousands of sequences from the same community. We conducted a study of diversity along a horizontal transect (ca. 120 km) and a depth profile (surface to bottom at ca. 2000 m) in the northwestern Mediterranean Sea, using this technology on the V6 region of the 16S rDNA gene and analyzed patterns of richness and evenness of marine free-living bacterial communities. A total of 201 605 tag sequences were obtained from the 10 samples considered and clustered according to their similarity in 1200 operational taxonomic units (OTUs) per sample on average. We found a parallel decrease in richness and evenness from coast to offshore and from bottom to surface. We also observed a predominance of a few OTUs in each sample, while ca. 50% of all OTUs were found as singletons, which indicated that the community structures differed dramatically between sites despite the relative proximity and the physical connectivity between the samples. Despite these differences, using the 300 most abundant OTUs only was sufficient to obtain the same clustering of samples as with the complete dataset. Finally, both richness and evenness were negatively correlated with bacterial biomass and heterotrophic production.