A total of six AP-PCR and AFLP primer combinations were used to study the genetic diversity in 55 Indian soybean varieties. The average numbers of amplified bands per assay unit were significantly (p<0.1) high for AFLP (121) than AP-PCR (82). The average number of polymorphic bands for AFLP (27.1) was significantly (p<0.1) higher than AP-PCR (17.6). The average polymorphism percentages for AP-PCR and AFLP were comparable. However, the average marker indexes of AFLP (8.5) primer combinations were significantly (p<0.1) higher as compared to AP-PCR (5.8), the high index was mainly attributed to high average number of bands, while the PIC values per assay unit of AFLP and AP-PCR were comparable. The study revealed that AFLPs are more efficient at revealing polymorphic loci than AP-PCR technique. Mantel’s tests for correlation using Jaccard’s similarity matrices between AP-PCR with combined AP-PCR+AFLP data and AFLP with combined AP-PCR+AFLP data was carried out and r = 0.8 and 0.9 were obtained respectively indicating strong significant correlation. The clustering of varieties in dendrogram generated by UPGMA analysis indicated no trend with respect to pedigree and common parentage analysis indicating that, two varieties derived from same cross might be diverse if the selection pressure operating is different. Over all genetic diversity in Indian soybean varieties was moderate, as revealed by AP-PCR, AFLP and AP-PCR+AFLP data.