A study of genetic diversity was conducted among four wild Arracacia species (A. elata, A. equatorialis, A. incisa and A. xanthorrhiza), using three accessions per species, 20 plants per accession referred to as a population, 100 morphological characters and five AFLP primer combinations producing 202 AFLP markers. Genetic diversity was well described using these morphological descriptors and AFLP markers. Analysis of molecular variance showed a total variation of 49.5% which was attributed to differences between species; variation between populations within species amounted for 25.8%, while variation within populations accounted for 24.6%. On the basis of morphological and molecular characteristics, accessions considered previously as A. equatorialis could be regrouped with A. xanthorrhiza. These comparisons and multivariate analysis resulted in the selection of 28 morphological characters considered as discriminant to identify the Arracacia species from Peru. According to our morphological and molecular analysis, three wild species of Arracacia genus were clearly identified: A. elata, A. incisa and A. xanthorrhiza. However, A. equatorialis which was not well identified botanically could be considered as very close to A. xanthorrhiza. © 2007 Springer Science+Business Media B.V.