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 ofFSHB gene.Results:The study results showed that there was genetic polymorphism with two different single strand conformation polymorphism patts, AA and AB. The former patt was associated with fertility in Egyptian buffaloes. Pair wise alignment of the two patts sequences revealed that FSHB patt 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.