The present investigation was undertaken to describe the relationships among species of Avicenniaceae family which have both economic and medicinal activities, collected in Indian Sundarban by the help of RAPD and ISSR markers. In this study, three different species of Avicennia genus were collected. Frozen young leaves (-200C) were taken to isolate the genomic DNA using a slightly modified CTAB method. For this experiment, a set of 10 RAPD and 10 ISSR markers were used to analyse the genetic diversity. The study showed that ISSR markers were more efficient than RAPD markers for polymorphism detection, polymorphic bands content per primer and total no of loci detection per primer as they were 75.53%, 11.9 and 15.6, for ISSR and 69.04%, 9.6 and 13.7 for RAPD, respectively. However, the observed no of alleles, effective no of alleles, Nei’s (1973) gene diversity and Shannon’s information index (I) were higher for RAPD (1.6087, 1.6087, 0.3043 and 0.4219, respectively) than for ISSR (1.5357, 1.4356, 0.2345 and 0.3357, respectively). However, no such reports on genetic diversity using ISSR markers were available in the genus Avicennia. The results of this study can be seen as a starting point for future researches aimed to develop phylogenetic tree using more samples and more molecular markers.