Objective: To study genetic variation in buffalo follicle stimulating hormone beta-subunit (FSHB) gene and its association with fertility. Methods: In this experimental study, blood samples were collected by standard methods using EDTA anticoagulant and transrectal ultrasound examination was conducted on fertile (n=74) and infertile buffaloes with a history of anestrum (n=30) or repeat breeding (n=12). The genomic DNA was extracted for PCR followed by single strand conformation polymorphism analysis. DNA sequencing was performed for the determination of single nucleotide polymorphism of FSHB gene. Results: The study results showed that there was genetic polymorphism with two different single strand conformation polymorphism patterns, AA and AB. The former pattern was associated with fertility in Egyptian buffaloes. Pair wise alignment of the two patterns sequences revealed that FSHB pattern II (AB) has C nucleotide insertion as SNP at the site of 208 bp of sequenced fragment. Conclusions: FSHB is polymorphic in the infertile Egyptian buffaloes, suggesting its practicability as a candidate marker for female fertility.