A fatal bulking phenomenon was found to occur occasionally in the methanogenic granular sludge of a mesophilic (35-40 degrees C), full-scale upflow anaerobic sludge blanket (UASB) reactor treating organic wastewater discharged from a sugar manufacturing factory. A vast number of filamentous cells were observed in the bulking sludge that were morphologically distinct from the previously recognized anaerobic bulking agent Anaerolinea thermophila. 16S rRNA gene-based analyses of the microbial populations in the bulking sludge revealed that the dominant filamentous organisms were members of proposed candidate bacterial phylum, KSB3. Fluorescence in situ hybridization (FISH) analysis of the healthy sludge granules showed that the KSB3 filaments were the dominant granule surface population suggesting that they are fundamental constituents of the sludge granules and that they occasionally overgrow in the reactor, possibly triggering the filamentous bulking. We surveyed 10 additional mesophilic and thermophilic anaerobic sludges for the presence and diversity of KSB3 populations. Bacteria closely related to the characterized KSB3 filaments were present in two types of mesophilically grown UASB sludge granules treating actual wastewater discharged from sugar-processing industries.