The present invention provides a high density Swamp Buffaloes {Bubalus bubalis) whole genome breeding chip and the application thereof. The high density whole genome breeding chip for Swamp Buffaloes reported in the present invention is 621800 SNP chip manufactured based on Affymetrix- technique. Each chip can detect 96 samples simultaneously and contains 621800 SNP sites. The marker sites have DNA sequences represented by Seq ID No. 1-621800. The chip can be used in molecular marker fingerprint analysis of the Development of High Density chip of Swamp Buffaloes (Bubalus bubalis) genetic resources, in genotype identification of the crosses of Swamp Buffaloes and River buffalo progenies, for genome wide association studies with traits of interest like milk yield, fat and protein percentage, somatic cell count and unlimited number of variables both natural as well as synthetic and having wide application prospects. The high density whole genome breeding chip has been specially designed and created for the development of a database for generation of prediction equation for selection of sires of high genetic merit in Swamp Buffaloes (Bubalus bubalis) for meat/ploughing.