In the present study the bacterial community structure in a sequencing batch reactor (SBR) operating in autotrophic conditions was determined in relation to temporal variations of NH4-N, NO2-N, NO3-N levels in the effluent. Bacterial richness and composition were determined by PCR-DGGE (Polymerase Chain Reaction - Denaturing Gradient Gel Electrophoresis) of 16S rRNA and amoA genes, and RISA (Ribosomal Intergenic Spacer Analysis) technique. The applied approaches revealed that the composition of bacterial population in the studied SBR varied in time. A positive correlation between Shannon index of ammonia-oxidizing bacteria (AOB) diversity and ammonia level in the effluent was observed. The variation of total bacterial diversity did not reflect the changes in nitrification efficiency.