Abstract: Background and Objective: Bruguiera is a mangrove species which commonly lives in the mangrove forest of Kemujan Island, Karimunjawa, Indonesia. The aim of this study was to evaluate the genetics of three morphologically similar brugueira and to determine the genetic relationship of the species. Methodology: Three morphologically similar species of Bruguiera cylindrica, Bruguiera gymnorrhiza and Bruguiera lyliadica were analyzed by RAPD (Random Amplified Polymorphic DNA) markers. DNA amplification was performed using five specific primers (OPA-01, OPA-02, OPA-03, OPA-04, OPA-05), PCR products were then analyzed using a Gel Analyzer and a dendogram generated numerically by the SIMQUAL association (Similarity for Qualitative) coefficient grouping method covered by UPGMA (Unweighted Pair Group Method with Arithmetic Mean) and computed with the NTSYSpc (Numerical Taxonomy and Multivariate Analysis System) programme. Results: Fifteen DNA polymorphism types were obtained, ranging from 100-400 bp, with primers OPA-01 and OPA-03 generating the most RAPD products, ranging in size from 154-384 bp. Conclusion: This study makes the first attempt to broaden existing knowledge of the three Bruguiera on the island of Kemujan are genetically different. The dendogram patterns of the three species could be grouped into two clusters, with B. cylindrica and B. gymnorrhiza being more closely related than B. lyliadica.