The genetic diversity and relationship among improved lines help maximize the use of available genetic resources, reduce genetic vulnerability and facilitate deployment of useful genes and thus broaden the genetic base of new varieties. Forty-one elite lines of mungbean developed during the last three decades were investigated using 80 mapped microsatellite markers for assessing the progress in genetic diversification in Indian mungbean breeding programme. In the analysis, 696 alleles were detected with an average of 8.68 alleles per locus. Gene diversity ranged between 0.93 and 0.05 with a mean of 0.68, and polymorphic information content ranged between 0.92 and 0.05, with a mean of 0.66. Out of 80 microsatellites, 51 were found highly polymorphic with > 0.60 PIC value and these were noticed as most informative. As a result of STRUCTURE analysis, three distinct genetic groups were identified and suggested that breeding programme led to a clear-cut improvement in 100-seed weight, pod length, seeds per pod and plant height in elite lines developed after the year 2000. The grouping pattern was also supported by the factorial and UPGMA analysis. These microsatellites covering all 11 linkage groups proved useful to detect genetic variation and assess the progress in trait improvement in mungbean breeding programme.