The Zunyi manganese deposits, which formed during the Middle to Late Permian period and are located in northern Guizhou and adjacent areas, are the core area of a series of large-medium scale manganese enrichment minerogenesis in the southern margin and interior of the Yangtze platform, Southern China. This study reports the universal enrichment of rare earth elements (REEs) in Zunyi manganese deposits and examines the enrichment characteristics, metallogenic environment and genesis of REEs. The manganese ore bodies present stratiform or stratoid in shape, hosted in the silicon–mud–limestones of the Late Permian Maokou Formation. The manganese ores generally present lamellar, massive, banded and brecciated structures, and mainly consist of rhodochrosite, ropperite, tetalite, capillitite, as well as contains paragenetic gangue minerals including pyrite, chalcopyrite, rutile, barite, tuffaceous clay rock, etc. The manganese ores have higher ΣREE contents range from 158 to 1138.9 ppm (average 509.54 ppm). In addition, the ΣREE contents of tuffaceous clay rock in ore beds vary from 1032.2 to 1824.5 ppm (average 1396.42 ppm). The REEs from manganese deposits are characterized by La, Ce, Nd and Y enriched, and existing in the form of independent minerals (e.g., monazite and xenotime), indicating Zunyi manganese deposits enriched in light rare earth elements (LREE). The Ceanom ratios (average ?0.13) and lithofacies and paleogeography characteristics indicate that Zunyi manganese deposits were formed in a weak oxidation-reduction environment. The (La/Yb)ch, Y/Ho, (La/Nd)N, (Dy/Yb)N, Ce/Ce* and Eu/Eu* values of samples from the Zunyi manganese deposits are 5.53–56.92, 18–39, 1.42–3.15, 0.55–2.20, 0.21–1.76 and 0.48–0.86, respectively, indicating a hydrothermal origin for the manganese mineralization and REEs enrichment. The δ13CV-PDB (?0.54 to ?18.1‰) and δ18OSMOW (21.6 to 26.0‰) characteristics of manganese ores reveal a mixed source of magmatic and organic matter. Moreover, the manganese ore, tuffaceous clay rock and Emeishan basalt have extremely similar REE fractionation characteristic, suggesting REEs enrichment and manganese mineralization have been mainly origin from hydrothermal fluids.