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Plectranthus hadiensis is an important medicinal plant in Sri Lanka. It was considered a separate species, P. zeylanicus, endemic to the island until its inclusion, as P. hadiensis var. tomentosus, together with morphs from southern Africa in the revised species concept of P. hadiensis. However, there are morphological, chemical, and therapeutic differences between the African and Sri Lankan morphs. We used eight molecular markers in a phylogenetic study to clarify the species concept of P. hadiensis and to investigate whether it should include the Sri Lankan morph. We examined the position of the two P. hadiensis morphs in relation to eight other Plectranthus species. The maximum likelihood tree revealed three clades: a weakly supported clade including P. calycinus, P. glabratus, P. fruticosus, and P. malabaricus; a highly supported clade including P. amboinicus and African and Sri Lankan specimens of P. hadiensis; and a highly supported clade formed by P. barbatus, P. caninus, and P. hadiensis var. tomentosus. The African P. hadiensis specimens form a highly supported subclade sister to a subclade containing the Sri Lankan P. hadiensis, suggesting that the subclades correspond to either two sister species or two subspecies. We propose that they are more likely to be sister species given the differences in morphology, chemistry, and chromosome number.