Mangroves, the intertidal ecosystems occurring primarily in the tropical regions of the world, are valuable natural resources with high productivity and unique habitat value. However, the genetic structure of plant species within the mangrove ecosystem is poorly understood. The present communication is the Þrst report on the use of molecular markers in assessing intra-site and intra-speciÞc polymorphism in one of the mangrove species, Acanthus ilicifolius, for identifying/ detecting distinct genotypes for long-term conservation. Random ampliÞed polymorphic DNAs (RAPDs) and restriction fragment length polymorphisms (RFLPs) were used to elucidate the intra- and interpopulation variability in this widely distributed mangrove species. In all, 48 genotypes representing eight distinct populations were analysed. A low level of polymorphism was detected at the intra-population level through both RAPD (3.8Ð7.3%) and RFLP (3.2Ð9.1%) analyses. At the inter-population level, 25 of the 73 RAPD loci (34%) detected through the use of 13 random primers and 44 of the 96 RFLP loci (45.8%) revealed through 15 probe/enzyme combinations were polymorphic. RFLP analyses were carried out using genomic clones developed from the same species. The somatic cells of the species displayed 48 chromosomes, with no numerical changes at either intra- or interpopulation levels.