Flehmen is frequently explained as part of male sexual behaviour, but it can also be associated with overmarking behaviour and thus individual recognition. We tested three explanatory hypotheses of flehmen behaviour: to detect sexual status of a female, to decide whether to overmark an individual, and to improve individual recognition. Additionally, we examined interspecific flehmen differences in the African equids. We observed 130 individuals of all 4 species among 15 groups in 5 zoos. We recorded 4445 eliminations: 142 were accompanied by flehmen and 1648 were inspected by another animal and followed by flehmen (n = 147 cases). As males of all age categories flehmened more often than females we conclude that flehmen serves to detect reproductive status of a female. However, this is not an exclusive explanation as animals of all sex and age categories flehmened when inspecting an elimination. Flehmen was not the predictor of overmarking. Nevertheless, we suggest that foals could use it for individual recognition. We found large interspecific differences with the highest rate of flehmen in African wild ass and least in mountain zebra. Thus, while the main function of flehmen is to detect female reproductive status, inter-individual and inter-species differences also play a role.