Aim: The mosaic of savannas that persists in the forest-dominant Congo Basin is thought to be palaeoclimatic relics, but past biogeographical processes that have formed and maintained these systems are poorly understood. Here, we explored the post-Pleistocene biogeography of Gabon's savannas using termites as biological indicators to understand historical and mechanistic factors influencing present-day termite communities in the country's extant savannas. Location Gabon, Central Africa. Taxon Blattodea: Termitoidae. Methods Using standardised transect methods, we sampled termite communities in four disjunct modern savanna areas of Gabon: the centre (Lopé), the southeast (Batéké) and the south (Mayombe North and South). Termites at Lopé were collected in three habitats (annually burned savannas, savannas with a depressed fire regime and forest). We used DNA barcoding of the COII region to identify termite species and compared abundance, species richness and community composition across areas and habitats. Results Community composition differed greatly between Lopé and both Batéké and Mayombe savannas with Lopé being exceptionally depauperate and lacking characteristic savanna species. Within Lopé, termite abundance and diversity was highest in forests and lowest in annually burned savannas, with a gradual change in species composition across the forest–savanna gradient associated with fire history. Main Conclusions The absence of savanna typical species in Lopé savannas challenges current assumptions that these savannas were linked to the south/southeastern savannas during the Pleistocene and suggests a different evolutionary history. Lopé savannas may instead have opened as an isolated grassland and never have been contiguous with neighbouring savannas, or were isolated soon after forest expansion began and have now lost savanna-typical species. Furthermore, the patterns of termite community composition in fire suppressed savannas support a hypothesis of rapid change driven by fire frequency where either fire suppression or infrequent burning over 23 years has meant savannas have become ecologically much more forest-like.