The prime objective of this book is to provide theoretical and practical data on the application of microsatellite markers in genetic characterisation of livestock breeds. This book contains the fundamental information on genetic diversity analysis and it provides better insight into the molecular characterization of animal genetic resources. This book describes the microsatellite-based genetic structure and relationship analysis. In this book, extraction of DNA, PCR amplification, genotyping of microsatellite markers, calculation of genetic parameters and bottleneck analysis are discussed in different chapters. The chapters have been illustrated with figure, tables, and photographs, wherever appropriate for easy understanding of the readers. This book will benefit post-graduate students and research scholars in the fields of Animal Genetics and Breeding and Animal Biotechnology to understand the concept of Microsatellite DNA genotyping for assessment of genetic variability in livestock.