Wild relatives of pigeonpea (Cajanus cajan L.) possess many useful genes that can be utilized for crop improvement, most importantly genes for resistance to Helicoverpa armigera, the legume pod borer. The present study aimed at quantifying diversity in a collection of Cajanus scarabaeoides, Cajanus sericeus, Cajanus reticulatus and C. cajan species selected from a wide geographic range using two PCR-based marker systems, amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSRs), and the hybridization-based restriction fragment length polymorphism (RFLP). Polymorphism was higher among the wild accessions than among the cultivated genotypes. Wild and cultivated Cajanus accessions belonging to different species clustered into four distinct major groups largely based on the interspecific differences. C. scarabaeoides accessions derived from same geographical origins formed one group reflecting similar genetic makeup of these accessions. Dendrograms generated using AFLP, RFLP and SSR marker data were comparable with minor clustering differences, which suggests that either method, or a combination of both can be applied to expanded genetic studies in Cajanus. Mantel testing confirmed the congruence between the genetic distances of three markers, indicating that the markers segregated independently, giving similar grouping patterns of all accessions having similar genetic origin.