This work aimed to search for single nucleotide polymorphisms of gonadotropin releasing hormone receptor (GnRHR) gene in Egyptian buffalo which involved in endocrine control of fertility. An ultrasonographic examinations of anestrum and repeat breeders’ buffaloes were performed prior to blood sampling through a transrectal ultrasonography. DNA was extracted from blood and the PCR and single strand conformation polymorphism (SSCP) techniques were adopted to study of GnRHR gene polymorphism. The PCR amplified a fragment with 240-bp in size and the SSCP results showed that there is a genetic polymorphism with three different patterns (AA, BB and CC) in Egyptian buffalo. The CC genotype was associated with smooth inactive ovary, while BB genotype was associated with fertility in buffalo. Multiple sequence alignment of the three patterns sequences revealed that GnRHR had 5 single nucleotide polymorphisms including one nucleotide insertion, one nucleotide deletion and 3 nucleotide substitutions. Insertion was at position 4 in pattern III. The deletion was at position 189 in pattern III, while the 3 nucleotide substitutions were at positions 204 (T/G), 206 (T/A) and 207 (A/T). In conclusion, GnRHR gene could be used as a candidate marker for fertility in Egyptian buffaloes with its mutation is related to ovarian inactivity.