Objective: This study was undertaken to find out the polymorphism variations in the estrogen receptor-a gene PvuII (rs2234693) and XbaI (rs9340799) in the different traditional Chinese medicine(TCM) syndromes of hypomenorrhea. Method: This case-control study used the polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) analysis to find out the results. Result: ①The differences of genotype frequencies of ESR1 rs2234693 PP/Pp/pp genotype carriers were statistically significant among the different TCM syndromes of hypomenorrhea. The ESR1 rs9340799 XX/Xx/xx genotype carriers were statistically significant too (P<0.001). The study showed that the genotype frequencies of ESR1 pp and xx genotype were higher in the kidney deficiency than other TCM syndromes of hypomenorrhea.②The differences of allele frequencies of ESR1 P/p and X/x genotype carriers were statistically significant (P<0.001) among the different TCM syndromes of hypomenorrhea. The study showed that the genotype frequencies of ESR1 p and x alleles werehigher in the kidney deficiency than other TCM syndromes of hypomenorrhea. Conclusion: The results of the present study suggested that the ESR1 rs2234693 and rs9340799 gene were associated with the different TCM syndromes of hypomenorrhea.Patients with high frequencies of the p allele and x allele were more likely to respond to the hypomenorrhea with the kidney deficiency syndrome. The study showed that the ESR1 pp genotype and xx genotype were more susceptible to the kidney deficiency syndrome of hypomenorrhea.