The efficacy of different strategies for controlling parasitic weeds depends on the level of awareness on the genetic structure of their populations. However, although Striga gesnerioides is a major threat to cowpea production in Burkina Faso, very few studies have focused on its genetic diversity at molecular level so far. This study has been designed in order to analyze the genetic diversity of Striga gesnerioides using microsatellite markers.Thirty ecotypes of Striga gesnerioides were screened with 36 microsatellite markers using the FTA card method for DNA extraction.The PCR products were revealed by electrophoresis on 3% agarose gel. The data were first processed by visual analysis of the migration profiles. The grouping of ecotypes was established using the Neighbour Joining (N-J) approach with Darwin version 6 software. Single and multi-varied statistical methods were used to assess the similarity and diversity between the samples studied and to calculate the genetic parameters of the different populations.The study revealed a moderate diversity within the collection. The fixation index (0.968) indicates high inbreeding. In addition, the low genetic distances between agroclimatic zones indicates genetically close populations.The cluster analysis identified 3 genetic groups. Genetic differences were also revealed between
some physiological races. The findings of this study will serve to develop new breeding and varieties dissemination
strategies for cowpea with regards to Striga gesnerioides.

Striga gesnerioides, genetic diversity, FTA cards, DNA, microsatellite markers.