Rust fungi taxonomically belonging to Pucciniales (Basidiomycota) are important phytopathogens that cause many significant diseases to agricultural crops and forest trees. Hitherto, ca. 8000 and 1200 species have been reported from worldwide and China, respectively. To investigate and document the diversity of rust fungi in China, we have sampled from 86 natural reserves and national parks in the past several years, and 6627 specimens have been collected. Our identification using both morphological and molecular data assigned 1654 collections to 337 species in 43 genera of 15 families, as cataloged in this paper. Among them, 34 new species are formally described based on their morphological distinctions and phylogenetic relationships. In addition, three new families Endoraeciaceae, Neophysopellaceae and Uromycladiaceae are proposed based on their morphological distinctions, phylogenetic independences and divergent times. Considering the traditionally morphologically defined families in Pucciniales have been increasing revealed to be discordant with phylogenetic groupings, taxonomic revisions are needed in future study to establish a natural classification system in Pucciniales. We also discussed the importance of morphologies in spermogonia and aecia for the delimitation of Puccinia and related genera. This study presents a significant contribution to the knowledge of rust flora in China. Taxonomic novelties: new families: Endoraeciaceae P. Zhao & L. Cai; Neophysopellaceae P. Zhao & L. Cai; Uromycladiaceae P. Zhao & L. Cai; new species: Chrysomyxa jinghongensis P. Zhao & L. Cai; Coleosporium sichuanense P. Zhao & L. Cai; Coleosporium smilacis P. Zhao & L. Cai; Cystopsora yunnanense P. Zhao & L. Cai; Gerwasia guanganensis P. Zhao & L. Cai; Gerwasia rubus-playfairianus P. Zhao & L. Cai; Hamaspora rubus-pirifolius P. Zhao & L. Cai; Macruropyxis guizhouensis P. Zhao & L. Cai; Macruropyxis paederiae P. Zhao & L. Cai; Melampsora hyperici-sampsonii P. Zhao & L. Cai; Melampsora linearis P. Zhao & L. Cai; Melampsora salicis-delavayanae P. Zhao & L. Cai; Neophysopella vitis-davidii P. Zhao & L. Cai; Phakopsora sophorae P. Zhao & L. Cai; Phragmidium nonapiculatum P. Zhao & L. Cai; Phragmidium kanas P. Zhao & L. Cai; Phragmidium duchesneae-indicae P. Zhao & L. Cai; Pileolaria medogensis P. Zhao & L. Cai; Puccinia amygdalus-iridis P. Zhao & L. Cai; Puccinia aphananthe-aspera P. Zhao & L. Cai; Puccinia microsorus P. Zhao & L. Cai; Puccinia nandina-domestica P. Zhao & L. Cai; Puccinia persicaria-odorata P. Zhao & L. Cai; Puccinia polygonum-aviculare P. Zhao & L. Cai; Puccinia pulverulentus P. Zhao & L. Cai; Puccinia saposhnikoviae P. Zhao & L. Cai; Puccinia sonchus-oleraceus P. Zhao & L. Cai; Puccinia thalictrum-finetii P. Zhao & L. Cai; Puccinia thalictrum-minus P. Zhao & L. Cai; Puccinia xingwenensis P. Zhao & L. Cai; Puccinia xinjiangensis P. Zhao & L. Cai; Puccinia zanthoxyli-chinensis P. Zhao & L. Cai; Uromyces aconiticola P. Zhao & L. Cai; Uromycladium yunnanense P. Zhao & L. Cai; new combinations: Chrysomyxa purpurea (C.J. You & J. Cao) P. Zhao & L. Cai; Neophysopella verannonae (Beenken) P. Zhao & L. Cai.