Despite their stability and the widespread use of enhanced biological phosphorus removal (EBPR), little is known about their microbial composition and activity. In our study we investigated highthroughput pyrosequencing of bacterial communities from two full-scale EBPR reactors of South Africa. Findings indicated that both EBPRs harboured high bacterial similarity, ranging from 83 to 100% with a diverse community dominated by Proteobacteria (57.04 to 79.48% for failed EBPR and 61.7 to 85.39% for successful EBPR) throughout the five selected treatment zones with the exception of the fermenter (Bacteroidetes: 55.84%) from the successful EBPR. However, a lower dissimilarity was observed with the presence of 70 unique bacterial genera from successful EBPRs belonging to Gammaproteobacteria, Betaproteobacteria, and Actinobacteria, while 69 unique genera from failed EBPR belonged to Alphaproteobacteria, Betaproteobacteria, and Clostridia. The failed EBPR (54.58%) revealed less fermenting bacteria in the fermenter as compared to the successful EBPR (73.58%). More detrimental organisms and less nitrifying/denitrifying bacteria were also found in failed EBPR than in the successful EBPR, as well as phosphate-accumulating bacteria. Canonical correspondence analysis (CCA) displayed a very low relationship between microbial patterns, pH and DO – suggesting that these environmental factors played a major role in community dissimilarity. Aerobic zones appeared to have the highest dissimilarity between both EBPRs, with the failed EBPR predominated by Acidovorax (26.2%) and the successful EBPR with unclassified Rhodocyclaceae (37.24%). Furthermore, 21.47% of readings (failed EBPR) and 17.18% of readings (successful EBPR) could not be assigned to taxonomic classifications, highlighting the high diversity level of novel microbial species in such an environment.