Genetic diversity analysis is a prerequisite for any crop improvement programme.This book is an original research work done by authors on pea and pigeonpea. Some selected varieties of each crop type were taken from all over India and analysed for genetic diversity. Brief description of various kinds of molecular marker types used in the study have been describe in the book. Technical details of some popular PCR based marker systems viz. RAPD and ISSR are emphasized along with their merits and demerits. Efficacy of each marker system used for detecting polymorphism in pea and pigeonpea, progeny relationships, genotype identification and species specific marker identification is described and compared. The statistical tools like, genetic distance measures, clustering methods, ordination methods etc. were used in the study.