The bacteria resident in sponges collected from Chuuk Lagoon and Kosrae Island of Micronesia were investigated using the 16S rRNA gene PCR-tagged pyrosequencing method. These sponges were clustered into 5 groups based on their bacterial composition. Diversity indexes and cumulative rank abundance curves showed the different compositions of bacterial communities in the various groups of sponges. Reads related to the phylum Chloroflexi were observed predominantly (9.7-68.2%) in 9 sponges of 3 groups and unobserved in the other 2 groups. The Chloroflexi-containing group had similar bacterial patterns at the phylum and lower taxonomic levels, for example, significant proportions of Acidobacteria, Gemmatimonadetes, SBR1093, and PAUC34f were observed in most members of this group. The three groups in the Chloroflexi-containing group, however, showed some minor differences in the composition and diversity. The other two groups contained high proportions of Proteobacteria (>87%) or Bacteroidetes (>61%) and different composition and diversity compared to the Chloroflexi-containing group and each other. Four pairs of specimens with the same species showed similar bacterial profiles, but, the bacteria in sponges were highly specific at the individual level.