Abstract: The genetic relationship of 80 Lilium species and cultivars was investigated at DNA level with SRAP（Sequence-related Amplified Polymorphism）marker. Fifteen polymorphic SRAP primers including 144 polymorphic loci were selected and hybrid embryo numbers was used to perform genetic structure analysis by Pritchard method. The total materials mentioned above were clustered into four main groups（gene pools） representing Asiatic hybrids and some wild species（S1），Longiflorum hybrids（S2），Oriental hybrids and others wild species（S3），and Oriental × Trumpet hybrids（OT）and another wild species（S4），which was consistent with the result of hybrids classification methods. Furthermore，genetic structure analysis revealed the pedigree between individuals better than traditional methods，and clarified the genetic relationship among species or cultivars. In addition，some cultivars from S3 groups as parents were used to hybridize，and significant correlations between the zygotic embryo numbers per 30 flower buds obtained from each cross combination as one of the indexes in crossing compatibility and absolute value of difference between female parent and male parent in main estimated membership coefficients was revealed. This research will be useful to select parents in lily breeding.

Key words: Lilium, genetic structure, SRAP, parents selection, grouping analysis