1. Describing the genetic structure and diversity of invasive insect pest populations is essential to better understand a species' invasion history and success throughout its distribution range. Tuta absoluta (Meyrick) (Lepidoptera, Gelechiidae) is a destructive pest of tomato and many other solanaceous crops, with very high economic impacts. Its invasion threatens food security in a large part of the globe, in areas such as sub-Saharan Africa where the agricultural resilience has already been weakened by rapid human-induced changes due in particular to population growth, increased trade and global change. 2. This work aimed to investigate the diversity and genetic structure of 60 populations of T. absoluta using microsatellite markers, with a particular focus on sub-Saharan Africa. 3. Our results revealed distinct differentiation and diversity patterns between T. absoluta native versus invaded areas, and high genetic homogeneity among the African populations sampled. However, for the first time, two weakly differentiated but distinct genetic clusters in Africa were identified. 4. The results suggest few introduction events of the species in Africa or multiple introductions from genetically close areas, significant gene flow between outbreaks and seem to indicate the existence of two distinct clusters in Africa. This new data enable us to formulate hypotheses on the species' invasion patterns and the dynamics of its invasive populations. 5. These hypotheses must be verified with more extensive sampling over the whole range of T. absoluta, especially in its presumed native area.