Abstract The study was carried out in Gir cattle for identification of genome wide SNPs and then to annotate the identified high-quality SNPs to the milk production traits. A total of 99 517 SNPs were identified with respect to the Bos indicus reference genome. Upon annotation of SNPs identified with respect to Bos indicus reference genome, 984 SNPs located in 175 candidate genes related with milk production traits, notably Acetyl-CoA carboxylase β gene, which affects milk composition traits by regulation of fatty acid oxidation in the mitochondria; Growth hormone receptor gene which have role in milk yield and its composition traits; LEP gene, involved in energy partitioning and metabolism, were among others. This study provides the first analysis of ddRAD sequences to discover SNPs in Indian Gir cattle breed, aligned to indicine reference genome. The variants mined in this study can be incorporated in existing SNP chips and thus, play an important role in understanding the genetic structure of our cattle in order to design appropriate breed improvement programmes.