A core sample comprising 141 wild accessions and cultivars of taro (Colocasia esculenta) grown in Southeast Asia and Melanesia, was described using six SSR loci that revealed a total of 87 alleles. Accessions clustered according to their geographic origin; a separation between S.E. Asia and Melanesia was revealed. The weak genetic structure observed also confirms the hypothesis of a narrow genetic base of cultivars. Using 16 additional SSR loci, the genetic structure of a sample of 39 accessions used as parents in the Vanuatu breeding programme was also described. An unexpected level of polymorphism was observed, with 2 to 18 alleles per locus. Levels of heterozygosity ranged from 45% to 90% with an average of 67.3%. The respective roles of sexual recombinations and clonality are discussed to better understand the organisation of the genetic diversity of taro.