This study was designed to find single nucleotide polymorphism (SNPs) in coding and non-coding region of PRKAA2 gene in Nili-Ravi and Kundi buffaloes. The PRKAA2 gene (AMPKα2) of 100 animals from both buffalo breeds were sequenced for SNPs identification. A total number of 43 inter and intra-generic SNPs were found. Out of which 17 SNPs were detected among buffalo breeds (intra-generic). All SNPs were intronic and may have a role in gene regulation and splicing patterns. These SNPs might be associated with commercially important production traits. This is the first study to identify novel SNPs that are linked to energy metabolism and production traits of buffalo.