The basidiomycete genus Armillaria causes root rot and death to woody plants in boreal, temperate and tropical regions of the world. Armillaria root rot has been described from various parts of Africa on many different hosts. However, very little is known regarding the evolutionary relationships among Armillaria species in Africa. The aim of this study was to determine the phylogenetic relationships between isolates originating from different regions in Africa using nDNA sequences from two non-coding gene regions. The ITS and the IGS-1 regions of the ribosomal DNA operon were sequenced and analysed using different phylogenetic tree searching methods. Phylogenetic trees grouped the African taxa in two strongly supported clades. One of these represented A. fuscipes and the other an undescribed but distinct species.