Objective This study accurately identified the existing varieties and calculated genetic diversity in Longnan City, Gansu Province, which was the main olive producing area in China, and provided a reference for the introduction, domestication, breeding and utilization of olive germplasm resources in China.

Method Identification and genetic diversity were analyzed for 110 individuals of 83 olive varieties collected from Longnan city using 13 SSR markers, and phenotypic diversity was analyzed with indicators such as leaf, fruit, and stone for 90 individuals of 68 varieties. And the clustering of varieties based on phenotypes was compared with that based on SSR markers.

Result The phenotypic diversity indices for olive varieties from Longnan were 1.83 for quantitative traits and 0.79 for quality traits, respectively; SSR markers identified 78 different genotypes for all olives analyzed, with an observed heterozygosity of 0.683 and an expected heterozygosity of 0.754, respectively; all varieties could be divided into three groups, and the grouping of varieties were more or less related with their origin; most of the varieties bred and selected in China were closer to those originated from Italy; compared with those in the phenotypic-based cluster tree, different individuals of the same variety were more inclined to cluster together in the tree based on SSR genotypes.

Conclusion In Longnan, 78 varieties with different genotypes were identified based on SSR markers, which shows a higher accuracy in variety identification and a clear kinship among varieties than that based on phenotypes. The phenotypic diversity and genetic diversity of olive in Longnan are high, and the introduced varieties are mainly from the western and central Mediterranean countries. Whereas the varieties bred and selected previously in China are more similar to varieties originated from Italy. To diversifying olive germplasm in Longnan, more varieties should be introduced and bred with varieties from different countries.