Resolving phylogenetic relationships within the economically important genus Coffea (Rubiaceae) has proven to be difficult due to low levels of plastid and nuclear ITS sequence divergence. The recent identification of a large number of conserved, single-copy, putatively orthologous genes (COSII) provides a unique opportunity to apply regions of the nuclear genome to phylogenetic studies of Euasterid species. We expand a previously published plastid data set of Coffea with the addition of three new plastid regions and a single COSII nuclear locus. Significant phylogenetic incongruence is identified between the plastid and nuclear COSII data sets, and a combined analysis is performed after removal of incongruent taxa. Phylogenetic results from plastid, nuclear, and combined plastid/nuclear data sets allow the novel identification of early diverging lineages in Coffea. Specifically, the data show that a group of predominately Lower-Guinea/Congolian Coffea species form a clade that is sister to the rest of the genus, and that the dry adapted baracoffea alliance from western Madagascar falls outside of previously defined East Africa/Indian Ocean and Indian Ocean clades. Well-supported patterns of phylogenetic incongruence are observed between plastid and nuclear data in several species, suggesting a potential role for hybridization in their evolutionary history. The results also provide further evidence for the paraphyly of African Coffea and support the supposition that the evolutionary history of the genus is more complicated than previously proposed.