AbstractCandidatusAccumulibacter phosphatis (CAP) and its sub-clades-level diversity has been associated and implicated in successful phosphorus removal performance in enhanced biological phosphorus removal (EBPR). Development of high-throughput untargeted methods to characterize clades of CAP in EBPR communities can enable a better understanding of Accumulibacter ecology at a higher-resolution beyond OTU-level in wastewater resource recovery facilities (WRRFs). In this study, for the first time, using integrated 16S rRNA gene sequencing, oligotyping and genome-resolved metagenomics, we were able to reveal clade-level differences in Accumulibacter communities and associate the differences with two different full-scale EBPR configurations. The results led to the identification and characterization of a distinct and dominant Accumulibacter oligotype - Oligotype 2 (belonging to Clade IIC) and its matching MAG (RC14) associated with side-stream EBPR configuration. We are also able to extract MAGs belonging to CAP clades IIB (RCAB4-2) and II (RC18) which did not have representative genomes before. This study demonstrates and validates the use of a high-throughput approach of oligotyping analysis of 16S rRNA gene sequences to elucidate CAP clade-level diversity. We also show the existence of a previously uncharacterized diversity of CAP clades in full-scale EBPR communities through extraction of MAGs, for the first time from full-scale facilities.