This study addresses geographic variation of body size and shape and of allele frequencies at 21 microsatellite loci in southern African populations of the desert locust, Schistocerca gregaria. These populations, which belong to the subspecies S. g. flaviventris, lack the capacity to change phase and to swarm relative to the northern populations of the nominate subspecies, S. g. gregaria. We reported overall genetic and morphological similarities among localities that cover most of the subspecies range. Of particular interest, the level of genetic diversity was moderately lower than in the swarming subspecies of the northern range. In addition, S. g. flaviventris populations were genetically homogeneous, such as observed in the northern range of the nominate subspecies. This result can be explained by north—southwest seasonal migration to follow rainfall.