Assessment of genetic diversity and identification of superior genotypes are the basic objectives of any crop improvement program. Earlier morphological and isozyme markers were used to assess the diversity, but these traits had an environmental influence. The recently developed molecular marker technology has opened up new vistas for the assessment of genetic diversity among genotypes at molecular level. In the present investigation, two multiloci markers viz., RAPD (25 primers), ISSR (11 primers) and one single locus marker viz., SSR (10 primer pairs) were used to assess the genetic diversity among 32 genotypes of pigeonpea, which included 23 cultivars and nine wild relatives. Diversity analysis was done with the help of statistics such as marker index, mean marker index, polymorphism information content, principal component analysis and dendrogram. The present study clearly elucidated the superiority of ISSR markers for genetic diversity studies over RAPD and SSR markers.