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Ethnopharmacological relevance The ethnopharmacology of Southwest China is extremely interesting because of the region's high level of cultural and medicinal plant diversity. Little work has been done to document the traditional medicinal practices in this area. This review aims to provide an overview of the current knowledge of how medicinal plants in this area are utilized, and conserved, in order to better understand the medicinal flora, identify research gaps, and suggest directions for further research. Material and methods A literature review was conducted that included peer reviewed journals, website, books, theses and scientific reports from 1979 to 2014. The distribution and characteristics of medicinal plant knowledge in each province, methods applied in research, and the fluctuations of literature in 5 year intervals were analyzed. The distribution research on different plant groups including fungi, ferns, mosses, and vascular plants were also analyzed. Results and discussion A total of 436 publications from 1979 to 2014 were selected for analysis. References were classified into three stages: discovery stage, utilization stage and conservation stage. Detailed results about the focus of the references, the methods applied, the development and relationship among all folk medicine in Southwest China, Daodi ethnomedicinal resources, Pharmacological studies and Toxicology studies were discussed. While, compared to the rich medicinal flora, the complex demographics and cultural diversity, a large gap still exist to fully understand and document the medicinal flora. Conclusions Based on the review results, most research efforts in Southwest China focused on the first step: discovery of traditional usage, geographical distribution, and taxonomy of medicinal species. Only a small percentage of traditional uses or treatments have been tested by modern ethnobotanical approaches. Further research needs to put more emphasis on identifying adulterations, evaluating of Daodi medicine, and elucidating effective compounds from traditional drugs, using molecular and phytochemical approaches. Knowledge on ethnic and cultural aspects of medicinal plant species, to develop effective conservation and sustainable use protocols is lacking. [ABSTRACT FROM AUTHOR]