<p><b>Background:</b> The genetic structure of a diverse set of 15 Indian indigenous breeds and non-descript indigenous cattle sampled from eight states was examined, based on 777 k single nucleotide polymorphism (SNP) genotypes obtained on 699 animals, with sample sizes ranging from 17 to 140 animals per breed. To date, this is the largest and most detailed assessment of the genetic diversity of Indian cattle breeds.</p> <p><b>Results:</b> Admixture analyses revealed that 109 of the indigenous animals analyzed had more than 1% <i>Bos taurus</i> admixture of relatively recent origin. Pure indigenous animals were defined as having more than 99% <i>Bos indicus</i> ancestry. Assessment of the genetic diversity within and between breeds using principal component analyses, <i>F</i> statistics, runs of homozygosity, the genomic relationship matrix, and maximum likelihood clustering based on allele frequencies revealed a low level of genetic diversity among the indigenous breeds compared to that of <i>Bos taurus</i> breeds. Correlations of SNP allele frequencies between breeds indicated that the genetic variation among the <i>Bos indicus</i> breeds was remarkably low. In addition, the variance in allele frequencies represented less than 1.5% between the Indian indigenous breeds compared to about 40% between <i>Bos taurus</i> dairy breeds. Effective population sizes (<i>N_e</i>) increased during a period post-domestication, notably for Ongole cattle, and then declined during the last 100 generations. Although we found that most of the identified runs of homozygosity are short in the Indian indigenous breeds, indicating no recent inbreeding, the high <i>F_ROH</i> coefficients and low <i>F_IS</i> values point towards small population sizes. Nonetheless, the <i>N_e</i> of the Indian indigenous breeds is currently still larger than that of <i>Bos taurus</i> dairy breeds.</p> <p><b>Conclusions:</b> The changes in the estimates of effective population size are consistent with domestication from a large native population followed by consolidation into breeds with a more limited population size. The surprisingly low genetic diversity among Indian indigenous cattle breeds might be due to their large <i>N_e</i> since their domestication, which started to decline only 100 generations ago, compared to approximately 250 to 500 generations for <i>Bos taurus</i> dairy cattle.</p>