Genetic diversity of ulluco (Ullucus tuberosus), maintained ex situ and originating from Peru and North Bolivia, has been analysed using morphological traits and inter-simple sequence repeat (ISSR) markers, along with passport data. With regard to morphological and ISSR variation, our study revealed a high number of morphotypes and genotypes. Morphological and molecular results were congruent and both correlated with geographical distribution. Moreover, comparison of molecular and morphological characterisation of accessions indicated the existence of intra-morphotype heterogeneity. We discuss the genetic structure of ulluco in relation to characteristics of the species and of the Andean agricultural system. Patterns of diversity probably have a geographical origin and have been modified for centuries by Andean farmers, at small and large scales. The fact that both morphological and molecular markers correlate with geographic distribution is of high interest for genetic diversity studies and for genetic resource conservation of Andean tubers and of other vegetatively propagated crop species. © 2009 Royal Botanical Society of Belgium.