The genetic diversity of 24 Iris lactea var. chinensis were analysed by using 100 ISSR primers of which only 11 primers generated distinct amplified products. Among the 24 materials, a total of 214 bands were detected, of which 170 bands were polymorphic. The percentage of polymorphic bands (PPB) was 79%. The ISSR-based genetic similarity (GS) values among 24 accessions ranged from 0.400 to 0.929. Abundant genetic diversity among I. lactea var. chinensis accessions was revealed by ISSR markers.Based on the UPGMA cluster analysis and principal components analysis (PCA), the 24 materials investigated were divided into four groups, most of genetic variation was within a group. Genetic distance was found to be related to geographic distance among I. lactea var. chinensis