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The arrangement of scutes on the carapaces of extant chelonians is very similar among species, but intraspecific deviations from typical scute patterns are common. Because intraspecific variation may relate to inbreeding depression, unfavourable egg incubation conditions and the presence of environmental pollutants, investigations of carapacial scute patterns in natural populations can enhance insight into the ecologies and survival challenges of chelonians. A population of the tortoise Homopus signatus, inhabiting an arid range with substantial annual rainfall variation, was sampled to record carapacial scute patterns. The typical pattern of H. signatus consisted of five vertebral scutes, four pairs of costal scutes, a cervical and a supracaudal scute, and 12 pairs of marginal scutes. Although it was expected that size classes (i.e. representing tortoises born in different years) and sexes would have different percentages deviations from the typical scute pattern as a result of different egg incubation conditions, percentages were similar among size classes and sexes. A high percentage of 44% (25% if counts of the relatively variable marginal scutes were excluded) of all tortoises had deviant carapacial scute patterns. Since the study population was situated in a relatively pristine area and supernumerary carapacial scutes appear related to egg incubation conditions in other chelonians, the wide variation in carapacial scute patterns in wild H. signatus may be the result of frequently challenging incubation conditions in the species’ harsh environment.