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.
Key words: Gaharu, Aquilaria sp., Gyrinops sp., genetic diversity, molecular marker, amplified
fragment  length polymorphism  (AFLP)