Lorantheae is the largest tribe within the Loranthaceae family. However, the relationships among genera of African Lorantheae have been poorly understood due to limited molecular data and taxon sampling in previous studies. Understanding phylogenetic relationships and developing a stable classification of the African Lorantheae requires a robust molecular phylogeny. To address this, we obtained complete plastomes, nuclear ribosomal DNA 18S-ITS1-5.8S-ITS2-26S, and mitochondrial sequences for 61 accessions using genome skimming data to attempt resolving recalcitrant relationships of this tribe within the African lineage. The sampling included representatives of all genera from the previous subtribal classification. Analysis of the plastome dataset resulted in a well-supported phylogeny with four clades. The topologies based on the plastome and mitochondrial datasets were generally congruent, only with minor discordance at the position of some genera. Topology of the nuclear ribosomal DNA was, however, not congruent with those from other datasets, with a few incongruent nodes detected. Our phylogenomic analyses largely resolve relationships in the tribe Lorantheae, supporting the monophyly of its subtribes and most of its genera, except for Agelanthus and Oncocalyx. Based on the well-resolved phylogenies, we propose two new subtribes and provide circumscriptions for the previous subtribes.