Genetic analysis of seventeen pigeonpea genotypes for fusarium wilt using twenty eight microsatellite markers produced 88 alleles. Difference in allele size was observed among resistant and susceptible genotypes. The average number of alleles per locus was found to be 3.14 the average PIC values was 0.49 using these microsatellite markers. The Jaccard’s similarity coefficients based on microsatellite markers data analysis was 0.49. A dendrogram constructed based on the UPGMA clustering method revealed two major clusters. Cluster-I comprised of nine cultivars and the cluster-II included remaining eight cultivars. Genotypes that are susceptible to fusarium wilt of pigeonpea viz., GT-1, GT-100, GT-101, GT-102, BANAS, AVPP-1, AGT-2, T-15-15 and LRG-41 formed one cluster. The dendogram showed that genotypes that are resistant to fusarium wilt of pigeonpea viz., C-11, BDN-2, ICPL-87, ICPL-87119, ICPL-84060, ICP-8863, BSMR-853 and WRGE-119 were closely related and they formed another cluster. The study revealed that microsatellite markers can be efficiently used for discriminating resistant and susceptible pigeonpea genotypes for fusarium wilt.