A composting product of marine animal resources has been used as a fertilizer and a soil conditioner in Japan. This compost was produced by a repeated fed-batch fermentation system with three successive aerobic bioreactors. Composting temperature reached about 75°C without heating. The bacterial diversity in this compost was investigated by denaturing gradient gel electrophoresis (DGGE) and sequence determination of the V3 region in the 16S rRNA genes. The sequence analysis showed that a majority of retrieved sequences corresponded to those of Bacillaceae, and we frequently found sequences similar to the 16S rDNA sequences of Bacillus thermocloacae and Bacillus thermoamylovorans. In addition, a bacterium antagonistic to a Fusarium strain was isolated from the compost. The isolate (Bacillus sp. NP-1) produced an antifungal compound, iturin A. These results suggest that this compost serves as a valuable source of plant growth-promoting rhizobacteria including the antifungal bacteria.