The microbial community structure of the biomass selected in two distinctly inoculated anaerobic oxidation of ammonium (anammox) reactors was investigated and compared with the help of data obtained from 454-pyrosequencing analyses. The anammox reactors were operated for 550 days and seeded with different sludges: sediment from a constructed wetland (reactor I) and biomass from an aerated lagoon part of the oil-refinery wastewater treatment plant (reactor II). The anammox diversity in the inocula was evaluated by 16S rRNA gene-cloning analysis. The diversity of anammox bacteria was greater in the sludge from the oil-refinery (three of the five known genera of anammox were detected) than in the wetland sludge, in which only Candidatus Brocadia was observed. Pyrosequencing analysis demonstrated that the community enriched in both reactors had differing compositions despite the nearly similar operational conditions applied. The dominant phyla detected in both reactors were Proteobacteria, Chloroflexi, Planctomycetes, and Acidobacteria. The phylum Bacteroidetes, which is frequently observed in anammox reactors, was not detected. However, Acidobacteria and GN04 phyla were observed for the first time, suggesting their importance for this process. Our results suggest that, under similar operational conditions, anammox populations (Ca. Brocadia sinica and Ca. Brocadia sp. 40) were selected in both reactors despite the differences between the two initial inocula. Taken together, these results indicated that the type of inoculum and the culture conditions are key determinants of the general microbial composition of the biomass produced in the reactors. Operational conditions alone might play an important role in anammox selection.