The genetic polymorphism of cyp19 and fshr genes might influence fertility performance in cattle and buffalo. This study used PCR-RFLP to pinpoint genetic variations in the cyp19and fshr genes and their relationship to the ovarian inactivity and silent heat in Egyptian buffaloes. Whole blood samples were taken in vacuum tubes that contain EDTA from female Egyptian buffaloes. Rectal findings and ultrasonography were carried out for 90 buffaloes and were divided into three equal groups, the 1^st group is smooth inactive ovaries, 2^nd group is silent heat and the 3^rd group is a control group. To analyze the genetic variations in the cyp19 and fshr genes, genomic DNA was isolated from blood. Amplification of a snippet of the cyp19 promoter and 230 bp of fshr exon 10 genes which were digested with PvuII and Hin1II (NlaIII) restriction enzymes respectively. Electrophoresis was used to examine the PCR-RFLP pattern, which revealed that all animals displayed the GG genotype as of 187 and 232 bp fragments except two of silent heat animals showed undigested monomorphic pattern at 419 bp which genotyped as AA. The PCR-RFLP pattern for fshr gene revealed that all the investigated buffaloes were polymorphic at 150, 200 bp and genotyped as GA except one silent heat animal has a monomorphic pattern at 230 bp with AA genotype. In conclusion, the current study revealed that there was no association between genetic polymorphism of cyp19 and fshr genes and reproductive disorders of Egyptian buffaloes especially ovarian inactivity and silent heat in Egyptian buffaloes.