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In Vanuatu, an oceanic archipelago located in south-west Pacific, taro (Colocasia esculenta (L.) Schott) is one of the staple crops. An ecogeographical survey of its genetic resources was conducted in ten villages, each located on a different island. A sample of 344 landraces referred as the National Sample (NS) was collected. Its genetic diversity was assessed using nine microsatellites markers and then was compared with an International Core Sample (ICS) that was previously distributed in the ten villages of the study in order to test the geographical distribution of allelic diversity as an effective mean for the on-farm conservation of root crops. The ICS was composed of 41 accessions, including 23 originating from South-East Asia. The molecular dataset revealed in the NS (1) 324 distinct multilocus genotypes, (2) six genetic clusters mainly differentiated by rare alleles, (3) a geographical structure of the genetic resources of taro based, within each village, on the dominance of one or two of these clusters rather that their exclusivity, and (4) an analogy between the patterns of dominant clusters between villages and the past and present social networks. In addition, accessions from the ICS revealed 52 new alleles. Based on these findings, we formulate hypotheses regarding the processes involved in the genetic diversification of taro in Vanuatu. We also discuss the use of this set of microsatellite markers along with the molecular dataset obtained from this study as effective tools to monitor the diversity and evolution of taro in the future.