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The genus Citrullus (Cucurbitaceae) consists of four species of desert vines. Two species (Citrullus colocynthis and Citrullus lanatus) are widespread weeds on several continents. Above ground, they can be relatively difficult to distinguish apart. However, Citrullus colocynthis is a perennial with a tuberous taproot, whereas Citrullus lanatus is an annual with a slender taproot. We studied the morphology and anatomy of taproot development to better understand their structural and ecological differences. The annual Citrullus lanatus reached close to its maximum taproot diameter (similar to 3mm) soon after germination. The vascular cambium formed four relatively broad triangular sectors of fibres in which were embedded relatively large diameter vessels. These sectors were separated by narrower triangular areas of secondary ray parenchyma. In contrast, the taproot diameter of the perennial Citrullus colocynthis continued to increase during the study, reaching similar to 20mm after 14 weeks. Most of this substantial root consisted of secondary xylem parenchyma, with a low density of relatively small diameter vessels and few fibres. The remarkable differences in root morphology and anatomy of the studied species of Citrullus are related to differences in their annual and perennial lifecycles. Interestingly, the slender taproots of Citrullus lanatus were calculated to have a similar theoretical hydraulic conductance to that of Citrullus colocynthis (large diameter taproot).