†Background and AimsThe phylogenetic relationships between species ofCoffeaandPsilanthusremain poorlyunderstood, owing to low levels of sequence variation recovered in previous studies, coupled with relativelylimited species sampling. In this study, the relationships betweenCoffeaandPsilanthusspecies are assessedbased on substantially increased molecular sequence data and greatly improved species sampling.†MethodsPhylogenetic relationships are assessed using parsimony, with sequence data from four plastid regions[trnL – Fintron,trnL – Fintergenic spacer (IGS),rpl16intron andaccD – psa1IGS], and the internal transcribedspacer (ITS) region of nuclear rDNA (ITS 1/5.8S/ITS 2). Supported lineages inCoffeaare discussed within thecontext of geographical correspondence, biogeography, morphology and systematics.†Key ResultsSeveral major lineages with geographical coherence, as identified in previous studies based on smallerdata sets, are supported. Other lineages with either geographical or ecological correspondence are recognized for thefirst time.CoffeasubgenusBaracoffeais shown to be monophyletic, butCoffeasubgenusCoffeais paraphyletic.Sequence data do not substantiate the monophyly of eitherCoffeaorPsilanthus. Low levels of sequence divergencedo not allow detailed resolution of relationships withinCoffea, most notably for species ofCoffeasubgenusCoffeaoccurring in Madagascar. The origin ofC. arabicaby recent hybridization betweenC. canephoraandC. eugenioidesis supported. Phylogenetic separation resulting from the presence of the Dahomey Gap is inferredbased on sequence data fromCoffea.