The genomic diversity of sixty three isolates of Moesziomyces penicillariae, the causal agent of smut of Pearl millet, was analysed using an ISSR (Inter Single Sequence Repeats) approach based on the universal minisatellite probe M13 [GAGGGTGGCGGTTCT (Karlsson, 1994)]. According to the electrophoretic patterns, the distance tree obtained indicates that the different genotypes from Senegal are divided into 4 clades. This genetic differentiation is correlated to the geographical origin of the isolates. Most of the isolates from the Northern areas formed a separate clade as well as those from the south. The isolate from Gambia is closer to those of the Southern of Senegal whereas those of Burkina formed an independent clade. The isolates from the Central and Eastern areas are distributed in two clades. However, in these regions, a higher genetic mix appeared: the distribution of the genotypes is not strictly correlated to their geographic origin. Our results point out that two major factors are involved in the geographic distribution of the populations of M. penicillariae in Senegal. Firstly, the genetic diversity is partly correlated to the climatic conditions in relationship to the Pearl millet varieties used in the different areas. Secondly, isolates sharing genetic markers were collected along the commercial ways, revealing that anthropochory has an important incidence in dispersal of the disease. These results highlight that the incidence of the smut disease of Pearl millet in Senegal must be controlled by using tolerant varieties adapted to the different climatic conditions and by the application of sanitary rules limiting the dispersal of infected seeds.