Alectra (Orobanchaceae) consists of primarily hemiparasitic herbaceous species distributed mainly in sub-Saharan Africa, with two species native to tropical America, and two widespread species extending out of Africa into India and China. Despite containing an economically important noxious agricultural weed, Alectra has never been the subject of a phylogenetic analysis. The monophyly of Alectra was assessed using DNA sequences from the nuclear (internal transcribed spacer) and chloroplast (rpl16, trnT-L) genomes, including 11 of 12 species. One of two holoparasitic species, Alectra alba, was placed outside of Alectra, supported as sister to a lineage containing the Asian holoparasitic genera Aeginetia Christisonia. Two highly supported lineages of Melasma were revealed: one containing the two included African species, and the other comprising the tropical American Melasma rhinanthoides and the single accession of the tropical American Escobedia. The placement of the Madagascan endemic Alectra fmticosa was shown to be unresolved in relationship to the remaining Alectra species and the two lineages containing Melasma. The monophyly of the remaining species of Alectra was highly supported.