The SRY protein has only one coding region and it is devoid of intron. PCR-SSCP analysis revealed nine polymorphic patterns in the SRY gene locus. The data presented provide a comprehensive view of the amino acids encoded by the SRY gene in the Indian Murrah buffaloes. A considerable change was observed in the amino acid production by the codons of the SRY gene between the Indian Murrah buffaloes and the Chinese Swamp buffaloes at nine different places. Any primer pair out of three sets of designed primers in this study can be used further for sexing of buffalo embryo/prenatal sexing. The study showed that there exists considerable genetic variation for SRY gene among the Murrah buffaloes which needs to be explored further in future studies with large samples.