In order to analyze the genetic differences and genetic background of natural hybrid progenies of tea, the molecular markers research was carried out based on 82 natural hybrid progenies of tea and 34 main cultivated varieties in Fujian by using 24 simple repeat sequence marks to analyze the genetic relationship, population genetic diversity and parental simulation analysis.The results indicate that (1) A total of 157 polymorphic sites were detected,with an average of 6.542 alleles,an average of 0.588 for nei''s diversity index and 1.182 for shannon information index,the mean values of observed and expected heterozygosity were 0.577 and 0.591,respectively. (2)The method of genetic distance clustered all the accessions into four groups, group one were mainly ‘Dangui’and the natural hybrid progenies of‘Dangui’, group two were mainly the Oolong tea varieties in Fujian and the natural hybrid progenies of ‘Dangui’,‘Huangguanyin’, group three were mainly‘Baijiguan’and the natural hybrid progenies of ‘Baijiguan’,group four were mainly the green tea varieties in Fujian. (3)The genetic distance between the natural hybrids of‘Dangui’,‘Baijiguan’,‘Huangguanyin’, and the main cultivar in Fujian were 0.079, 0.117 and 0.107 respectively.(4)The simulated parents were mainly the oolong tea variety in Fujian, the genetic identity, genetic differentiation index and gene flow between subgroup b of group one and subgroup a of Group two were 0.899、0.043 and 5.480 respectively.(5)AMOVA attributed about 88.52% of the variance to individuals within populations, indicating that the main genetic variation existed within populations.