The abundance and phylogenetic diversity of the microbial community in the hydrogenetic ferromanganese crust, sandy sediment and overlying seawater were investigated using a culture-independent molecular analysis based on the 16S rRNA gene. These samples were carefully collected from the Takuyo-Daigo Seamount, located in the northwest Pacific Ocean, by a remotely operated vehicle. Based on quantitative PCR analysis, Archaea occupy a significant portion of the prokaryotic communities in the ferromanganese crust and the sediment samples, while Bacteria dominated in the seawater samples. Phylotypes belonging to Gammaproteobacteria and to Marine group I (MGI) Crenarchaeota were abundant in clone libraries constructed from the ferromanganese crust and sediment samples, while those belonging to Alphaproteobacteria were abundant in that from the seawater sample. Comparative analysis indicates that over 80% of the total phylotype richness estimates for the crust community were unique as compared with the sediment and seawater communities. Phylotypes related to Nitrosospira belonging to the Betaproteobacteria and those related to Nitrosopumilus belonging to MGI Crenarchaeota were detected in the ferromanganese crust, suggesting that these ammonia-oxidizing chemolithoautotrophs play a role as primary producers in the microbial ecosystem of hydrogenetic ferromanganese crusts that was formed as precipitates from seawater.