A verdant strip of urban and peri-urban agriculture (UPA) lines the banks of the River Nile at Khartoum (Sudan), but little is known about its physical structure and species composition. This study was conducted in 120 gardens, covering 160 ha at the urban locations of Tuti Island and Shambat and the peri-urban location of El Halfaya to determine the extent and plant composition of UPA gardens in Greater Khartoum, which includes the cities of Khartoum, Khartoum North and Omdurman. The survey identified 84 plant species from 35 plant families, of which 47 were utilised as crops predominantly for commercial production of fruits, vegetables, spices and condiments, grains, and fodder. The gardens of Tuti Island, where production of lime (Citrus aurantiifolia (L.) Swingle) was widespread, had a mean species richness of 1.7 and a Shannon index of 0.4. The gardens of Shambat, where leafy vegetables were common, had higher crop diversity levels with a mean species richness of 4.4 and a Shannon index of 1.2. The gardens of El Halfaya, which was the only location where the production of some spices and condiments was recorded, had a mean species richness of 3.7 and a Shannon index of 1.0. All three study locations were largely dominated by monocultural commercial production relying heavily on external inputs. The four groups of gardens distinguished by cluster analysis were cultivated by 21 ethnic groups, 46% of the surveyed households relied on additional off-farm income and gardens supplied 12% of household food. Economic and ecological benefits of the studied UPA gardens might be enhanced if crop diversity and structural complexity of these gardens were increased.