The structure of Accumulibacter lineage was examined over a three-year period in six full-scale wastewater treatment plants and compared to the population in a laboratory-scale reactor. The Accumulibacter lineage reached 69% of all bacteria in the laboratory-scale reactor and contained clades IA and IIA,C,D only. In full-scale plants, Accumulibacter constituted up to 12%, correlated with sludge loading with BOD, COD, N and P. Clade IA was more abundant after periods with low temperatures, whereas clades IIA,C,D presented opposite variations. The fraction, unrevealed by clade-specific probes, constituted 31–62% of the Accumulibacter lineage in all but one full-scale plant – the population in the plant with significant industrial contribution in the influent resembled the low diversity in the laboratory-scale reactor. Selection of specific clades in the laboratory-scale reactor was associated with its different performance, despite stable operational conditions being maintained through the study. It implies that high relative abundance of Accumulibacter in bacterial community is not enough for efficient P removal and the effectiveness may also be associated with the presence of specific clades. A considerable fraction of Accumulibacter in full-scale plants, which is not targeted by clade-specific probes, should be further investigated to better characterize clades that may affect effectiveness of phosphorus removal.