The African fan palm or toddy palm (Borassus aethiopum Mart.) plays a significant role in rural village economy because of the many uses of different parts of the plant for food, construction, traditional medicines and crafts. However, some of these uses which specifically target either male individuals (construction beams) or reproductive stages (fruits and hypocotyls) put pressure on the genetic diversity of palm populations and threaten the species as a whole. As a preliminary step to defining conservation strategies for Borassus aethiopum populations in Benin, an assessment of their genetic diversity was conducted through the use of microsatellite markers. In the absence of molecular resources for this species, we first set out to evaluate the transferability of microsatellite primers that had previously been designed in other palm species, including the cousin species from Asia Borassus flabellifer. We show that the portability of such markers, quantified as their ability to successfully amplify B. aethiopum DNA, is very low. Moreover, among the successfully transferred primers we found that the ability to detect polymorphisms, both within or among nine fan palm populations sampled across the Beninese territory, was even lower. In light of these first results, we discuss experimental options that will allow us to overcome this technical difficulty, and the future development of our project throughout the West African subregion.