This study was held with the aim to identify single nucleotide polymorphisms (SNPs) in leptin gene and their influential effect on milk traits in Azikheli buffaloes from Swat, Pakistan. Two fragments of sizes 958bp and 828 bp were amplified covering leptin gene intron 1 to exon 3 using polymerase chain reaction (PCR) following Sanger sequencing. In the study, 41 SNPs were identified in both low and high yielding population in which 30 SNPs showed significant association with milk yield and fats. Among these, g.12027T>C, g.12084G>A and g.12157T>G in intron 1 showed strong positive correlation while g.11864A>C/G in intron 1 and g.14092T>C in intron 2 negatively correlated with both milk yield and milk fats. Three non-synonymous SNPs, g.12235Aleptin gene variants had a significant effect on the milking ability of Azikheli buffaloes. These polymorphisms can be used as genetic markers for improving the milk production practices in dairy industries.