This study employed 454-pyrosequencing to investigate microbial and pathogenic communities in two wastewater reclamation and distribution systems. A total of 11972 effective 16S rRNA sequences were acquired from these two reclamation systems, and then designated to relevant taxonomic ranks by using RDP classifier. The Chao index and Shannon diversity index showed that the diversities of microbial communities decreased along wastewater reclamation processes. Proteobacteria was the most dominant phylum in reclaimed water after disinfection, which accounted for 83% and 88% in two systems, respectively. Human opportunistic pathogens, including Clostridium, Escherichia, Shigella, Pseudomonas and Mycobacterium, were selected and enriched by disinfection processes. The total chlorine and nutrients (TOC, NH₃-N and NO₃-N) significantly affected the microbial and pathogenic communities during reclaimed water storage and distribution processes. Our results indicated that the disinfectant-resistant pathogens should be controlled in reclaimed water, since the increases in relative abundances of pathogenic bacteria after disinfection implicate the potential public health associated with reclaimed water.