Fomitiporia oboensis (Hymenochaetaceae, Basidiomycota) is described from the Western African, Equatorial island of São Tomé. The species is characterized by cushion-shaped basidiomes, (5–) 6 (–6.5) pores / mm, absence of setae, basidiospores mostly 7.0–8.0 × 6.5–7.0 µm (ave = 7.4 × 6.8 µm), and inhabiting cloud forest (elev. ~1900 masl) at São Tomé. Phylogenetic inferences based on four DNA loci (5' end of the 28S, ITS-5.8S, partial Tef-1, and RPB2) show that the species forms a distinct, terminal clade, affine to F. aethiopica, F. tsitsikamensis, and a fourth undescribed taxon known from a single specimen originating at ~ 3000 masl at Mt Elgon, Kenya. These four species inhabit high elevation forests of the Afromontane archipelago and share a phylogenetic background. Phylogenetic inferences also show that these species share close genetic backgrounds with taxa occurring further North in Mediterranean Europe and Central Asia and, more globally, with Fomitiporia species of the Holarctic lineage. The affinities of the African Fomitiporia are discussed.