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Musa beccarii N.W.Simmonds var. beccarii and Musa beccarii N.W.Simmonds var. hottana Hakkinen were described earlier in Acta Phytotaxonomica et Geobotanica based on their morphological characteristics. In order to distinguish the genomes between the two M. beccarii varieties and M. coccinea Andrews, we have now studied them with the Inter-Retrotransposon Amplified Polymorphism (IRAP) marker analyses. The high levels of IRAP polymorphism detected in this study showed that M. beccarii var. beccarii and M. beccarii var. hottana are two distinct varieties. Additional IRAP bands found in M. beccarii var. beccarii indicated that M. beccarii var. hottana might be evolutionarily more ancient than M. beccarii var. beccarii because LTR retrotransposons are not transpositionally removed.