The combined molecular markers including InDel,ESTSSR and SSR were used to analyse the genetic diversity of 94 lotus germplasms introduced in Kunming region. The results showed that a total of 204 bands were amplified by the 60 pairs of primers screened,and 233 alleles were detected. The average Shannon’s index of the three markers was more than 0.8,the index of gene diversity was above 0.52,indicating that the detection rate of diversity is high.The result of Mantel test showed that the correlation r values between the combined markers and each independent marker were all higher than 0.789 4. Ninetyfour germplasms were divided into 5 groups with cluster analysis and population structure analysis of combined markers,which was related to traditional classification and provenance classification. There were obvious differences in genetic diversity between American lotus and Asian lotus. According to genetic composition,SinoAmerican hybrid lotus is distributed in American lotus or Asian lotus. In summary,the 94 lotus resources introduced to Kunming are rich in genetic diversity,and the combined molecular markers have a high detection rate of diversity in lotus germplasm resources. It will provide germplasm resources and technical support for further selecting and breeding elite lotus varieties.