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The sesame (Sesamum indicum) breeding program of Kasetsart University aims to improve the quality and quantity of sesame yield. Nine varieties, comprising 4 black sesame varieties, namely,‘KU-Sr6040’, ‘KU-18’, ‘KU-21’ and ‘CM-07’, and 5 white sesame varieties, namely, ‘KU-19’, ‘KU-20’, ‘CM-53’, ‘Cplus-1’ and ‘Cplus-2’, were released for farmers. Sesame is a self-pollinated crop. Seeds of released varieties are easily multiplied by farmers and others. On the other hand, the seed may be used for commercial benefit in an illegal way. To protect national benefits, the issuing of sesame plant patents should be seriously considered in the near future. To protect breeder’s right, genetic marker technology is highly suitable to identify improved sesame varieties. The objective of this project was to introduce DNA fingerprinting for 9 sesame varieties developed by the sesame breeding program of Kasetsart University. DNAs of the above 9 varieties (‘KU-Sr6040’, ‘KU-18’, ‘KU-21’, CM-7, ‘KU-19’, ‘KU-20’, ‘CM-53’, ‘Cplus-1’ and ‘Cplus-2’) were extracted and DNA fingerpriting, AFLP (amplified fragment length polymorphism), performed the polymorphisms of each variety. Forty-eight primer pairs were applied in this study. The results showed that 16 polymorphic bands obtained from 6 primer pairs, namely, TaqI-AGA/MseI-CTG, TaqI-AGT/MseI-CAC, TaqI-ACT/MseI-CTT, TaqI-ACT/MseI-CTG, TaqI-ATG/MseI-CAT and TaqI-AGC/MseI-CAC, could be used to distinguish all 9 sesame varieties. So, these DNA fingerprints from 6 primer pairs were used for sesame identification and variety registration.