Lethal control of stock-raiding predators is generally assumed to have fewer consequences for the species’ population dynamics if it involves males only. However, very little data are available that assess whether shot ‘‘problem’’ animals indeed are essentially males. In this study, we used two independent genetic methods (four X-chromosomal polymorphic microsatellite loci and the sex-specific ZFXY marker) validated against known-sex samples to determine, from skin samples collected over a 6-year period, the sex of 59 leopards (Panthera pardus) shot by farmers in Botswana. We found that out of 53 leopards that could be sexed genetically, 21 were females (39.6 %); males were thus not significantly more often shot than females. Comparing the genetically determined sex of shot leopards to that reported by farmers showed that 58.3 % were mistaken for the opposite sex. Our genetic study revealed that more females than presumed are hunted in response to alleged livestock predation. With females frequently misidentified as males, the current practice of shooting ‘‘problem’’ animals is likely to negatively affect the population dynamics of leopards. These genetic data may be used to guide the development of a revised management policy for large-carnivore hunting. Importantly, models of sustainable harvest need to include female offtake as a parameter.