The present study aimed to describe the bacterial community present at an anaerobic up flow bioreactor with ANAMMOX activity, inoculated with the sludge from the anaerobic pond of a swine slurry treatment system. The description was based on the molecular DNA techniques using primers for amplification of complete 16S rRNA gene and also new primers to amplify smaller fragments from 16S rRNA. During the bioreactor operation time, the bacterial community changed significantly, increasing the nitrogen removal efficiency, reaching after 500 days a removal rate of 94%. The complete PCR amplification of 16S rRNA gene generated 17 clones, where three presented similarity with Candidatus Jettenia asiatica (97%), twelve with Janthinobacterium (99%) and two with uncultured clones. The PCR amplification of 436 base pairs had generated 12 clones, of which eight presented 96-100% similarity with Candidatus Anammoxoglobus propionicus, Planctomycete KSU-1 and one with Pseudomonas sp. (99%) and three with uncultured clones.