By contrast with the strain undergone by amphibian and reptile populations today, broadly documented in the scientific literature, the Quaternary fossil record of these groups is very conservative. In order to establish the non-human-induced effect of climate change on herpetofaunal diversity, we collect data from Pleistocene sites of the Sierra de Atapuerca complex (Burgos, Spain), which records the last few million years of changes. Diversity of herpetofauna communities present in this period was measured in terms of richness and evenness indexes. Both indexes were performed independently for amphibians and reptiles and also for the whole population. Finally, the relation with the climatic parameters was analysed, with OLS regression models. The highest diversity (richness and evenness (1-D)) occurred in periods considered analogues of the current interglacial, whereas minimum diversity values were reached during periods when conditions were harsher. In all cases, the diversity values were always restored subsequently, pointing to great resilience. Temperature proves to be the most influential climatic factor. Accordingly, amphibians and reptiles have been able to overcome previous climatic changes successfully. By contrast, the effects of anthropization have generated an uncommon loss of diversity, the like of which has not been seen in the last few million years.