This paper presents a simple and practical method for stratifying taro germplasm based on morpho-agronomical characters. More than 450 accessions of taro collected throughout Vanuatu and established in a field collection were described using 19 descriptors. A hierarchical approach was used to stratify the agro-morphological variation. Three sampling strategies were tested and the variation captured within each sample was compared for the frequencies of characters. The first sample (Si) was randomly selected; the second sample (S2) was conducted within the subgroups produced by the stratification method, and the third sample (S3) was based on UPGMA clustering within each subgroup. AFLP markers were used to compare the diversity between S3 and a fourth sample (S4) that included the parents of the Vanuatu breeding programme, and more diversity was found in S3. AFLPs were found to be useful to validate the hierarchical approach used for stratification. These studies have confirmed the narrow genetic base of the Vanuatu taro germplasm. They have been useful for detecting duplicates and fingerprinting of accessions.