Among many hypotheses in the literature that explain overmarking in mammals, most studies favour a sexual selection hypothesis. However, results in the literature are conflicting. In this study, we tested two hypotheses that could explain overmarking by males: (i) as a part of sexual selection, more specifically to mask scent of receptive females and (ii) as a form of communication serving to aid group cohesion. We observed each of the three zebra species in eight different herds at four zoos. In total, we recorded 1395 eliminations (760 defecations, 635 urinations) performed by 78 individuals including 8 stallions. Stallions investigated 248 eliminations and overmarked 124. The rate of overmarking by stallions was higher than those of all other sex and age categories. Stallions of all species overmarked all age and sex categories, except Grevy’s zebra stallions did not overmark foal eliminations. In contrast to our first hypothesis, when attracted to the elimination, stallions overmarked non-oestrus females more often than oestrus ones. Thus, our results did not support the hypothesis that overmarking by males has a sexual selection function, but it could be explained by the group cohesion hypothesis. Based on our results, it seems that overmarking by equid males plays a greater role in intra-specific communication than in intra-sexual competition. In addition, this behaviour might play different roles in different species based on their social organisation.