There are more than 6 000 clones of Hema brasiliensis Mull. Ary germplasm in the germplasm garden of Chinese National Key Biotechnology Laboratory for Tropical Crops and some of them are elite germplasm demonstrated by production and previous studies. AFLP (amplified fragment length polymorphism) fingerprinting analysis was performed on 25 clones (15 of Wickham clones and 10 of Amazon wild clones which possess phenotypes with high-yielding,/Iow-yielding, cold-tolerance/cold-sensitivity, oidium-resistance/oidium-sensitivity, tapping panel dryness (TPD) /healthy) respectively through a 377 DNA sequencer (P. E. Corp.) and PAGE electrophoresis results were analyzed by using GeneScan(TM) and Genotype(TM) Analysis software (P. E. Corp. The fragment profiles of different clones were obtained. Five hundred and eighteen fragments were generated by two primer combinations screened from 64 primer combinations and 511 fragments appeared to be polymorphic (98.6%). Genetic distance ranged from 0.25 to 0.81 between clones and ranged from 0.07 to 0.17 within RRIM600 clone. A specific 320 bp fragment of the oidium-resistant clones was found through genotype analysis. These results showed that AFLP fingerprints were highly reproducible and powerful and can be widely used in germplasm identification and genetic diversity analysis of Hema brasiliensis. In addition, based on the AFLP data, cluster analysis was performed. Cluster results showed that all the clones studied were almost clustered into a group one by one.
