The alkaline phosphatase-harboring community (the phoD community hereafter) plays an important role in organic P mineralization. Here, we comparatively studied the biogeographical patterns of abundant and rare phoD subcommunities and their roles in mediating soil phosphatase (ALP) activity and available P content in three representative steppe regions in China, namely the Inner Mongolian Plateau, the Loess Plateau, and the Qinghai-Tibetan Plateau. The results indicated that soil ALP activity, available P content, soil and microbial biomass C:P, N:P ratios varied significantly among steppe regions. Significant differences in diversity, metabolic energy and assembly processes were observed between abundant and rare phoD subcommunities. First, richness of the rare taxa was significantly higher than that of the abundant subcommunities. Second, testing of metabolic theory of ecology showed that rare subcommunities had a higher metabolic activation energy than the abundant taxa. Thirdly, deterministic other than stochastic processes dominated in the community assembly of both subcommunities. Soil pH was the key environmental determinant in community assembly processes for both subcommunities. The relationships among P-cycling parameters and between these parameters and phoD diversity were scale-dependent. The phylogenetic beta diversity of the rare phoD taxa had higher correlations with P-cycling parameters than that with the abundant taxa. More rare than abundant genera were significantly correlated with P limitation and ALP activity at different spatial scales. The rare Frankia was the key genus detecting P limitation, producing ALP and enhancing soil available P in Qinghai-Tibet.