Five different artichoke hybrid populations (crosses between a male sterile artichoke (MS6) and three American accessions (AMA3, AMA7, AMB1) and two Spanish accessions (SP2, SPA2)) plus a commercial hybrid population (Opal F1, Nunhems, Netherlands) were used for molecular and morphological characterisation in order to identify the purity of the F1 populations. Molecular analysis was carried out using the inter-simple sequence repeat (ISSR) technique with twenty primers. Out of these, nine were polymorphic, producing 82 DNA bands per primer on average, 56 of which were polymorphic among the populations. A dendrogram, drawn on the basis of a similarity matrix using the UPGMA algorithm, revealed that the 66 samples (10 plants per F1 populations and their respective progenitors) could be classified into two major clusters at a Nei’s genetic distance of 0.13. The male parents were genetically quite similar to all their respective progenies. In order to confirm hybrid purity, only the primers which amplified bands specific to the male parent of each hybrid were considered and the inheritance of the single locus for each cross-combination was analysed. Three ISSR markers (857c, 857g and 878) were able to confirm the hybrid purity. The morphological trait analysis showed that eight of the 17 morphological characters were significantly different among the six F1 populations. When the Mantel test was applied to the matrix of the Nei’s genetic distances and the matrix of morphological traits, a significant degree of correlation was observed between them. A selection method using ISSR markers based on cluster analysis is suggested to confirm the purity of artichoke hybrids and to predict the characters expected by any F1 hybrid offspring. © 2010 Springer Science+Business Media B.V.