Direct evidence for Central African vegetation history is mostly derived from palynology and palaeolimnology. Although anthracology has proven worthwhile for palaeovegetation reconstructions in temperate regions and South America, charcoal analysis has hardly been applied for Central Africa. Moreover, a transparent charcoal identification procedure using large databases and well defined characters has never been developed. Therefore, we present a Central African charcoal identification protocol within an umbrella database of species names and metadata, compiled from an on-line database of wood-anatomical descriptions (InsideWood), the database of the world's largest reference collection of Central African wood specimens (RMCA, Tervuren, Belgium) and inventory and indicator species lists. The 2909 Central African woody species covered by this database represent a large fraction of the total woody species richness of Central Africa. The database enables a directed search taking into account metadata on (1) anatomical features, (2) availability of thin sections within the reference collection, (3) species distribution and (4) synonymy. The protocol starts with an anatomical query within this database, focussing on genus rather than species level, proceeds with automatic extension and reduction phases of the resulting species list and ends with a comparative microscopic study of wood reference thin sections and charcoal anatomy. In total, 76.2% of the Central African species in the database are taken into consideration, focussing on indicator and inventory species. The protocol has a large geographical applicability, as it can be optimised for every research area within Central Africa. Specifically, the protocol has been optimised for the Mayumbe region and applied to radiocarbon dated (2055–2205 14C yr BP) charcoal collections from a pedoanthracological excavation. The validity of the protocol has been proven by the mutual consistency of charcoal identification results and the consistency of these identification results with vegetation history based on phytogeographical and palynological research within and around the Mayumbe. As such, anthracology complements palynology and a combination of both can lead to stronger palaeobotanical reconstructions.