Chickens are agriculturally important animals and valuable model organism. Many inbred lines of chickens are well characterized for disease resistance and production traits. In general, biodiversity can be described at several levels from phenotypic observations to molecular data. Recent advances in molecular technology have opened up new horizons in assessment of genetic variability at the DNA level. Microsatellites are a group of DNA markers which are widely used to study genetic biodiversity in chicken. In present book, at first, we have reviewed application of different DNA markers in studying biodiversity in chicken; then different microsatellite markers have been used to study among and within genetic diversity of six Indian chicken populations. This book can be especially useful for students and researchers who are willing to know microsatellite analysis in chicken more in details.