Balanites aegyptiaca (L.) is one of the priority fruit trees for rural communities in the West African Sahel and plays a multifunctional role in the daily life of the populations. However, very few studies have been done in Niger on the morphological diversity of B. aegyptiaca populations particularly considering farmers’ perception. The main objective of this study was to identify the morphotypes of B. aegyptiaca populations in the southwestern part of Niger. The survey was conducted in the Dosso region. The study revealed that local communities in the study zone have extensive traditional knowledge on B. aegyptiaca. Forty-one (41) morphotypes were identified according to farmers’ perceptions. Indeed, the local population relies on the observable variations of different parts of the plant, notably the fruits, the leaves, the taste of the fruits and the flowers to classify the morphotypes. Nevertheless, it should be noted that farmers do not combine traits from different parts of the plant to discriminate phenotypes. This poses a serious challenge in the classification of B. aegyptiaca by farmers, as the same morphotype can be classified differently according to the socio-professional activity of the respondent. It is therefore necessary to carry out additional molecular analyses to confirm farmers’ designations.