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This study contributes the first genome size data for wild populations of Cynara cardunculus, the presumed progenitor of artichoke and cultivated cardoon. C-values estimated by flow cytometry are 2C = 1.98–2.14(3.03) pg for wild cardoon (10 populations), 2C = 2.10–2.11 pg for cultivated cardoon (two accessions) and 2C = 2.05 pg for artichoke (one accession). Chromosome counting (carried out for all material except the artichoke) establishes diploidy in all accessions. In order to provide a phylogenetic framework for Tunisian populations, internal transcribed spacer (ITS) region was sequenced and analysed together with previously published Cynara sequences. The wild and crop cardoons present similar karyological features and genome sizes despite strong morphological differentiation, with the single exception of a Tunisian population (from Tajerouine), which exhibits a 42–53% higher genome size. Along with Sicilian individuals, Tunisian wild C. cardunculus appear genetically closer to artichoke and cardoon than to studied wild relatives from the remaining distribution. This highlights the crucial importance of taking into consideration the North African territory in deciphering the history of C. cardunculus crop domestication.