Objective Genetic diversity of Fortunella hindsii germplasms was analyzed to facilitate resource utilization and breeding.

Methods A collection of 108 F. hindsii germplasms was organized based on 13 agronomic traits and 10 pairs of SSR molecular markers. The characteristic genetic variations of the collection were analyzed according to the calculated variation coefficient, polymorphism information content (PIC), genetic differentiation index (F_st), and other parameters combined with the analysis of molecular variance (AMOVA) and clustering.

Results The phenotypic differentiation of F. hindsii was rich with the variation coefficients ranging 10.51%–50.79%. There were 41 alleles detected in the SSR markers, averaging 4.1 alleles per locus. On average, the population showing a PIC of 0.459 (locus B18 being the highest at 0.729), a Shannon's information index (I) of 0.945, an observed heterozygosity (Ho) of 0.324, and an expected heterozygosity (He) of 0.515 was genetically rich in diversity despite some degrees of inbreeding. It was clustered into 5 subpopulations without apparent correlation with the geographical distribution. The genetic variations revealed by AMOVA mainly originated within an individual germplasm at 53% and among individuals at 31%. The genetic differentiations among the subpopulations ranked from moderate to high with F_st = 0.071–0.226. Among the subpopulations, GroupⅠtopped the rest with an F_st＞0.18.

Conclusion The 108 F. hindsii germplasms demonstrated with high genetic diversity. The SSR markers applied for the analysis satisfactorily rendered the information needed for further studies on the resource conservation and breeding program.