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The phylogenetic relationships of Nolana (Nolaneae, Solanaceae) were constructed using partial sequences (ca. 891 bp) of the granule-bound starch synthase I (GBSSI) or the waxy gene. Nolana, with 89 species, is primarily distributed in coastal Chile (49 spp.) and Peru (43 spp.), and of these, four species are recorded in Peru and Chile, and another from the Galapagos Islands, Ecuador. Our phylogenetic analysis, utilizing a sampling of 63 of the 89 species, supports the monophyly of Nolana and recovered three clades with 95%-100% bootstrap support. Nolana sessiliflora is the sister taxon to the remainder of the genus. Two large, highly supported clades are evident; one containing taxa from Chile, Peru and the Galapagos Islands, and another containing taxa from Chile and Peru. Nolana galapagensis, an endemic to the Galapagos Islands, is suggested to be sister to N. arenicola in a clade that also includes N. adansonii from southern Peru and northern Chile. These two species differ substantially in habitat preference, habit, leaf shape, and mericarp morphology. The monophyly is confirmed for a morphologically cohesive group composed of N. acuminata, N. baccata, N. elegans, N. reichei, N. parviflora, N. pterocarpa, and N. paradoxa, a clade of essentially Chilean species.