Objective  This paper aims to reveal the genetic diversity of natural populations of Chionanthus retusus in different regions of China, and to provide a scientific basis for rational protection development and utilization.

  Method  The genetic diversity and population genetic structure of 62 samples from 7 Chionanthus retusus natural populations in different regions were studied using sequence related amplified polymorphism (SRAP) molecular marker technique.

  Result  Seven natural populations of Chionanthus retusus had higher genetic diversity, and 8 pairs of SRAP primers amplified a total of 1 728 clear bands, of which 1 649 were polymorphic, and the percentage of polymorphic bands (PPB) was 95.43%. The number of effective alleles between populations was 1.213 7, the diversity of Nei’s gene was 0.153 7, and the information diversity index of Shannon’s was 0.268 0. There were higher levels of intra-population genetic variation and lower levels of inter-population genetic variation among natural populations of Chionanthus retusus (Gst = 0.133 6), and higher levels of gene flow among seven natural populations of Chionanthus retusus (Nm = 3.243 7). The genetic similarity coefficient between Chionanthus retusus populations ranged from 0.898 0 to 0.973 6, with an average of 0.934 4. The Mantel test (r = 0.288, P = 0.205) and the clustering among populations proved that there was no significant correlation between genetic distance and geographical distance among populations. The clustering results of 62 primary germplasm showed that most of the germplasms were characterized by the fact that most individuals in the same population came together, and some germplasms had the phenomenon that individuals of different populations gathered together, showing that the genetic variation between populations was relatively stable and the level of genetic variation within the populations was relatively high, which was consistent with the results of genetic diversity analysis.

  Conclusion  Comprehensive multi-factor analysis speculated that Taihang Mountain area may be the main producing area of Chinese Chionanthus retusus germplasm resources.