The study of genetic diversity in buffaloes, particularly in Kalimantan, is crucial for their survival and breeding. The assessment of buffalo genetic diversity in this book uses mitochondrial DNA D-loop assessment to identify genetic variability among populations. High genetic diversity is more likely to breed and reduce undesirable traits. This book assesses the level of genetic diversity in three buffalo breeds in Kalimantan, validates phylogenetic analyses and assesses the genetic structure of the buffaloes. This will facilitate the future development and genetic management of these species. In particular, this book will use mitochondrial D-loop sequences as a means to trace ancestral biodiversity across multiple locations. Ultimately, the results can be used to refine and improve genetic potential that can also be applied to develop livestock production systems through phenotypic and genotypic functions of selected Kalang buffaloes.