Aquilaria sp. (Thymelaeaceae) is the most valuable non wood production of forestry plant in Indonesia. It produces a fragrant resin when subjected to fungal attack and has been traded Internationally known as gaharu. Knowledge of genetic diversity and relationship among species and genus is important for breeding purposes and species conservation. In this study, genetic variability of six Aquilaria species were analyzed using the AmplifiedFragment Length Polymorphism (AFLP) markers. Ten AFLP primer combinations amplified 1353 DNA fragments ranging in size from100 to 350 bp of which 1285 (95%) of them were polymorphic. Genetic similarities among Aquilaria sp. consisted of A. malaccensis, A. beccariana, A. microcarpa, and A. crassna ranged from 63.90 to 72.00 % based on Dice coefficient. The dendrogram derived by the unweighted pair group method with arithmetic mean of germplasm analysis were clustered into two main groups. Hence, a genetic variation among species is quiet high. Bootstrap values for the groups supported 70% of the cluster using a linear relationship equation of (r = 0.724, P < 0.0001) was observedbetween known pedigrees and AFLP-derived genetic similarity for 136 pairwise comparisons of Aquilaria species. For example, A. malacensis and A. microcarpa have the highest genetic similarity (72.00%) compared with another Aquilaria species. Primer pairs E-ACG/M-CTA produced a specific fragment for A. beccariana (850 bp), A. crasna (550 bp, 180 bp, and 140 bp), A. malaccencis (1500 bp), A. microcarpa (250 bp) and Gyrinops versteegii (150 bp). Primer pairs E-ACG/M-CAA produced a specific DNA fragment only for A. beccariana (1500 bp and 100 bp). Primer pairs E-ACC/M-CAC also produced only specific fragment for A. crassna (1500 bp). Study showed the usefulness of AFLP analysis in Aquilaria sp. and its potential application for breeding and species conservation. Further, molecular diversity estimated in the present study combined with the datasets on other morphological/agronomic traits will be useful for selecting the appropriate accessions for plant improvement through conventional and molecular breeding approaches.