Lantaneae are an example of a taxonomically problematic, widespread and recently radiated Neotropical lineage. Taxonomy in Lantaneae is difficult because of complex, overlapping patterns of shifts in morphological traits among members; monophyly of the traditional genera cannot be assumed without additional information from molecular data. We took a multi-locus approach to infer phylogenetic relationships in Lantaneae, resolving major clades among a broad representative sample that covers the morphological, taxonomic and geographical diversity of this group. Data from multiple, independent loci reveal individual gene trees that are incongruent with one another, with varying degrees of support. Without reliable, applicable methods to determine the sources of such incongruence and to resolve it, we present the consensus between well-supported topologies among our data sets as the best estimate of Lantaneae phylogeny to date. According to this consensus tree, fleshy fruits in Lantaneae have been derived from dry fruits at least five times; taxonomic schemes separating genera based on fruit characteristics are artificial. Lantaneae have shifted into the Neotropics from the southern temperate subtropics and have colonized Africa in at least two separate long-distance dispersal events. This study provides a first pass at a broad Lantaneae phylogeny, but two important areas remain unresolved: the position of Acantholippia relative to Aloysia; and species-level relationships in the Lantana–Lippia clade. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ●●, ●●–●●.