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Little is known about vegetative morphological diversification in Neotropical plant clades in comparison with diversification of reproductive characters. Phylogenetic relationships of the Neotropical Heliotropium (Heliotropiaceae) were studied using sequences of nrITS and four plastid regions (trnL-trnF, trnS-trnG, trnH-psbA, rps16). Vegetative morphological diversity (leaf morphology, habit), measured as amount of morphospace occupied and as variance of individual characters, was compared among the clades resolved and between groups of species inhabiting dry and humid areas. Three well-supported clades were recovered: (1) Heliotropium sect. Heliothamnus from the tropical Andes; (2)Heliotropium sect. Cochranea from the Peruvian and the Atacama Deserts; and (3) the Tournefortia clade, comprising the remaining American sections of Heliotropium and the mainly Neotropical Tournefortia sect. Tournefortia. Phylogenetic discordance detected between the plastid and nuclear partitions may have been due to lineage sorting, hybridization or differences in number of informative sites. Morphological diversity was largest in the Tournefortia clade and tended to be greater in dry than in humid areas, but without statistical support. Heliotropium sect. Cochranea was as diverse as the Tournefortia clade in leaf morphology and may have experienced adaptive radiation in the Atacama Desert. Lowest vegetative diversity was found in Heliotropium sect. Heliothamnus. The infrageneric delimitation in Heliotropium needs reassessment.