The Kei-apple (Dovyalis caffra) is an indigenous fruit with excellent nutritional characteristics that renders it a suitable candidate for novel food and beverage products. As an indigenous species, the Kei-apple has been studied only to a limited extent with particular emphasis on fruit characteristics important for agro-processing applications. A specific knowledge gap in the published literature relates to the inability to distinguish between male and female trees at the juvenile stage. This limitation hampers orchard management plans which require a specific ratio of male:female trees to ensure adequate pollination and fruit production. Furthermore, collection of specimens from the wild is also compromised by the inability to distinguish between sexes. Therefore, the present study investigated the suitability of two complementary methods, i.e. characterisation using molecular markers and DNA content analysis via flow cytometry, in order to distinguish between male and female trees. The molecular markers allowed for the identification of putative male and female specific markers and the DNA content analysis revealed differences in the average estimated nuclear DNA content of male and female trees. However, molecular markers did not allow for sex discrimination in 100% of the tested samples (i.e. in 70–94%) and the difference in the DNA content between the sexes was small. This may be resolved by testing additional markers or refining the flow cytometry method, however, until such time, it is recommended that future applications use both methods to limit the risk of misidentifications.