The causes of spatial distribution gaps for a given species may be either both natural (habitat discontinuities) or non-natural (local extinctions, inaccurate knowledge). These species are defined as 'gap species'. We analyzed the country checklists for African chelonians in order to identify both gap species and gap countries. We also compared patterns observed in chelonians with those observed in African small mammals. Species richness was highest in South Africa, Congo, Nigeria, Tanzania, Angola and Ghana, and the countries exchanging the smallest number of species with neighboring countries were South Africa and Congo. The main gap countries were Togo, Benin, and Congo. Moist savannahs, tropical forests, and swamp areas were inhabited by significantly higher numbers of gap species. Body size of gap species was significantly larger than that of non-gap species, possibly due to bush-meat consumption. Increases in the number of gap species per country were significantly correlated between chelonians and small mammals. There was a significantly positive relationship of turnover rates by paired countries between chelonians and rodents as well as between chelonians and insectivores, and the mean turnover rates by country were highest in Sudan and Chad, whereas the whole southern portion of Africa and part of West Africa had low mean turnover rates. The high number of gap species in Congo, Central African Republic (C.A.R.), and Cameroon may be due to suboptimal research, and in Togo and Benin may depend on the Dahomey Gap. The tropical forests and the moist savannahs are the most important habitats for both groups.