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Biological control of crop aflatoxin contamination with atoxigenic <i>Aspergillus flavus</i> is very successful in US agriculture. Atoxigenic lineages of <i>A. flavus</i> are used to reshape fungal communities so that average aflatoxin-producing potentials are reduced. These community modifications are associated with large reductions in crop aflatoxin content. We have been adapting this technology to aflatoxin management in sub-Saharan Africa. Development of locally and/or regionally directed biocontrol products requires precise information about diversity, distribution and lineages of potential biocontrol isolates with differential adaptations. SSR analyses were performed on 1798 L-strain isolates of <i>A. flavus</i> obtained from Benin, Burkina Faso, Ghana, Kenya, Mozambique, Nigeria, Senegal, Tanzania and Zambia. Number of isolates analyzed differed among countries, but similar genetic diversity was observed in each country based on 17 SSR loci. Over 1000 atoxigenic haplotypes of potential value in biocontrol were detected. Many haplotypes were restricted locally, but certain haplotypes were widely distributed. Although some signals of local adaptation were detected, all major genetic lineages included isolates from several countries, suggesting substantial migration. While the SSR diversity in each country was high, significant linkage disequilibrium and minimum spanning network suggest clonal reproduction and mutation are primary forces shaping the observed population structure.