Abstract: Species catalogue provides basic data of a biota in a natural geographical region or an administrative division, and is the premise of biodiversity research and conservation, as well as the rational utilization of botanic resources. However, because of ongoing advances of plant taxonomy and systematics research, and different taxonomist viewpoints, botanical references adopt different plant systems and taxonomy. Species catalogue therefore needs continuous updates. This study conducts a rigorous evaluation and review of the source data collected from Flora of Yunnan, Checklist of Yunnan Seed Plants, Flora of China and other taxonomic references ranging from monograph, herbarium to field investigation, through which the catalogue of seed plants in Yunnan Province (version 2016) was built. This is the most authoritative and accurate catalogue recording information of seed plants in Yunnan so far, which can not only facilitate the research, conservation, and rational utilization of seed plants, but also provide a basis for biodiversity management and policy-making. The dataset covers 16,064 species of seed plants in Yunnan, which fall to 2,392 genera under 253 families. These include 113 species of gymnosperms (including infra-species, 105 when infra-species are excluded) affiliated to 25 genera under 9 families, and 15,951 species of angiosperms (including infra-species, 14,433 when infra-species are excluded) affiliated to 2,367 genera under 244 families. The dataset consists of four parts of data: family name in Latin, family name in Chinese, species name in Latin and species name in Chinese.