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Abstract Background Xishuangbanna of Yunnan Province, southwest of China belongs to a global biodiversity and cultural hotspot. Agrobiodiversity plays an essential role in local livelihoods and traditional culture in the region. However, preliminary studies suggest that diversity of crop plants and livestock species is declining. We hypothesized that agrobiodiversity and traditional means of preserving agrobiodiversity are threatened because of changes in government policy in favor of commercial plantations, land use change and changes in traditional agricultural practices. We investigated whether or not agrobiodiversity was declining, the specific causes, and signs of active biodiversity conservation practices in ethnic minority communities of Xishuangbanna which could form the basis for extensive in situ conservation programmes. Methods A series of field studies to document trends in agrobiodiversity were conducted in different ethnic minority communities in Menghai County, Mengla County and Jinghong City of Xishuangbanna of Yunnan Province, southwest of China between July 2015 and February 2016. Data was obtained through the use of semi-structured questionnaires, field observation and participatory rural appraisal (PRA) tools. A total of 360 ethnic households provided information on current status, functions, characteristics, changes, and threatened factors of farming crop and livestock resources. Some measures for in situ conservation of agricultural biological resources were also researched using PRA methods. Results Two hundred twenty-six crop varieties belonging to 31 families, 71 genera and 101 species were identified in Xishuangbanna, which included 83 vegetable crops, 77 food crops, 24 spice crops, 22 fruit crops, 13 cash crops, 6 oil crops, and 1 cloth crop, respectively. There were 15 livestock varieties, belonging to 6 major species: cattle, pigs, goats, chickens, ducks, and geese. Different crop and livestock resources had their own characteristics, functions and threatened factors. Since 2002, agroecosystem, crop diversity and livestock diversity have declined greatly over the Xishuangbanna region as a whole under implementation of the Sloping Land Conversion Program (SLCP). Swidden agriculture was completely eliminated under this program and gradually replaced by large land areas devoted to rubber, tea and banana plantations. Villager numbers engaging in farming production and population of crops and livestock were greatly decreased, particularly in terms of production of local traditional varieties. However, some in situ conservation measures such as seeds preservation, planting of traditional crops and raising livestock have played an important role in local agrobiodiversity conservation. Conclusion Abundant agricultural resources and agrobiodiversity are critical to the local livelihood and maintenance of traditional culture in Xishuangbanna. However, agrobiodiversity and related traditional culture have been greatly impacted by implementation of the SLCP since 2002. Therefore, in future conservation of agrobiodiversity, incorporating some sustainable protection measures based in local communities such as convening seed exchange fairs, conserving traditional varieties in permanent plots, making a visual documentary of indigenous cultivation, and providing traditional agricultural products to tourists should be carefully considered and adopted.