Abstract: Analysis of diversity by citrus based microsatellite set in Aegle marmelos (L.) Corr. was undertaken because molecular markers are DNA based markers and reveal the genetic diversity which is more universal. Genetic diversity of A. marmelos was measured by using 10 microsatellite markers. A total of 47 alleles were detected in A. marmelos across the 10 loci investigated, all these alleles were polymorphic, thus revealing a level of 100% polymorphism. The number of observed alleles assorted flanked by 4 to 7 with mean 4.7±1.059 alleles at each locus. The experimental no. of alleles intended for every 10 loci gone beyond the effectual no. of alleles that assorted between 1.384 and 3.164 with an average value 1.995±0.11. In present study the mean observed heterozygosity was 0.127+0.06, which was not more than heterozygosity (expected). The expected heterozygosity varied from 0.164 (CCSM147) to 0.685 (CT19) with mean value 0.407±0.177. Since, observed heterozygosity is less than the expected heterozygosity seems to be due to inbreeding.