Abstract: The paper aims to understand the source of local potato varieties and name confusion problem in Yunnan Province. Field investigations, plant morphology observations, cytoplasmic genome polymorphism molecular marker detection and analysis, relevant historical literature digging methods were used to comprehensively investigate the sources and effects of 16 local potato varieties in Yunnan Provinces. It was showed that: (1) The local varieties were mainly distributed in poverty-stricken high altitudes mountainous areas with minorities living. (2) These local varieties were morphological characterized by flower type and color, tuber shape and skin/flesh color, plant type and leaf shape, and the presence of homonym and synonyms was common. (3) We also found abundant polymorphisms of chloroplast/mitochondrial genomic DNA (cp/mt DNA) among these local varieties, including W/α(D), W(A)/β, T/β, and W/γ(D), four kinds of cytoplasm types. (4) Potato was carried into Yunnan in the middle of 18th century. The introduction of local potato varieties in Yunnan Province was mainly related to the entry of western missionaries, the migration and distribution of ethnic minorities, the reformation of local communities, the opening and development of ethnic minority communities. This research reveal the source and the transmission routes of local potato varieties in Yunnan, understanding the important impact on the economic, social structure and cultural development, to better innovate potato breeding since the background of potato became the staple food in China.