Human domesticated cattle genetic resources nearly 8,000 to 10,000 years ago. ). A total 1,019 cattle breed is present around the world. This study gives a detailed assessment of genetic diversity in Pakistani cattle breeds from different agro ecological zones and genotyped for 500,939 autosomal single nucleotide polymorphism (SNP). Mean minor allele frequency (MAF), which were 0.23, 0.20, 0.22, 0.22, 0.20, 0.18, 0.20, 0.22, 0.21 and 0.18 for Achi, Bhagnari, Cholistani, Dhanni, Dajal, Kankrej, Lohani, Red Sindi, Sahiwal and Tharparkar cattle, respectively. Across all breeds 64% SNP markers were observed polymorphic (MAF > 0.05) within breeds and remaining 36% were considered as monomorphic markers. Experiment 2 discussed the two different approaches, selective sweep and population differentiation index (FST), to identify selection signatures between and within breeds in Pakistan. First method was used to detect haplotypes fixation on genomic regions within breeds. Second, FST was used to identify genomic regions having different allele frequencies between these breeds. The melanocortin 1 receptor (MCIR) gene was found on BTA 18 at 147, 573, 32-147, 590, 82 bp for Lohanni breed. This gene was previously associated with an adaptive trait in Bos indicus. A number of putative genes linked with productive traits (LAP3, CAPN3, CYP19, SAR1B, and RPS6KA2), reproductive traits (PIK3CA, SPERT, and IGF1R), nervous system (KIT, FGF5, ASIP and HSPB9) and immune response (IL2, IL4, SERPINA3-8 and BOLA3) were identified as being under selection. Experiment 3 examined population genetic properties of copy number variations (CNV). High resolution results of CNV revealed genome wide admixture proportion and agro-ecological variation pattern within and among these breeds. We detected 53 CNV regions and these regions overlapped with genes involved in traits related to immune response, body size and parasitic resistance. This could provide possible genetic relationship among these Pakistani indigenous breeds and other cattle breeds of the world. It is important to mention that small sample size of this study may not be truly representative of the whole population and could lead erroneous conclusion about the entire population. This study might be used properly and conserved in order to manage with unpredictable future environments. Moreover, a genomic understanding of natural selection how and where has shaped the genetic pattern of these breeds in Pakistan was exposed by loci identified that are important to the development of these breeds. The results of this study make a foundation for more suitable application of selective breeding and conservation approaches of Pakistani cattle breeds.