Background and Objectives: The species to the Lannea genus are trees, shrubs with compound leaves. Thus, individuals called atypical Lannea with single leaves and of socio-economic interests have been identified in the central plateau region (Burkina Faso). This study aimed to contribute to the identification of atypical species. Material and Methods: The Polymerase Chain Reaction (PCR) method using specific primers was performed and consisted of extracting DNA from young leaves of Lannea individuals, amplifying and then sequencing portions of discriminating DNA (matK, rbcL and rps16). Results: It was shown that individuals belong to the Lannea genus, but are subdivided into three subgroups: a first subgroup containing Lannea microcarpa and two subgroups with no previously identified Lannea species. Conclusion: These atypical individuals are ecotypes or mutants of Lannea microcarpa.