Abstract:Yunnan province is the refuge and birthplace of magnolias, the primitive and evolutionary species of Magnoliaceae are distributed alternately in there. It is very important to study the phylogenetic evolution and classification of Magnoliaceae.In this study, ISSR molecular markers were used to study 48 species of Magnoliaceae wild plant resources in Yunnan province.The results showed that a total of 151 bands and 151 polymorphic bands were amplified from the 10 primers, and the percentage of polymorphic bands was 100%. The total number of observational alleles (Na), effective alleles (Ne), Nei"s genetic diversity index (H) and Shannon"s information index (I) of the 48 Magnoliaceae plants were 2.0000, 1.5645, 0.3379 and 0.5101, respectively. The total genetic diversity index (Ht) was 0.3680 and the intergeneric genetic diversity index (Dst) was 0.2519. The intergeneric genetic diversity accounted for 68.4% of the total genetic diversity index. The coefficient of gene differentiation (Gst) was 0.6840, and the gene flow (Nm) was 0.2310. 48 species of Magnoliaceae plants were divided into 7 groups by the UPGMA clustering, and the clustering results were not consistent with the classification of genera, but distributed in different genera.and Magnolia rostrata, Michelia flaviflora and Michelia sphaerantha may be the ancestors of Magnoliaceae in Yunnan province.The 48 species of Magnoliaceae wild plants in Yunnan province have high genetic diversity in general, but they have high inter-genus genetic variation and small gene flow, which may lead to the risk of genetic drift. Moreover, the clustering results are different from the classification system of Liu Yuhu.The results provide an important basis for the origin, evolution and classification of Magnoliaceae at the molecular level.