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Background  Groundnut pre- and post-harvest contamination is commonly caused by fungi from the Genus  Aspergillus .  Aspergillus flavus  is the most important of these fungi. It belongs to section  Flavi ; a group consisting of aflatoxigenic ( A. flavus ,  A. parasiticus  and  A. nomius ) and non-aflatoxigenic ( A. oryzae ,  A. sojae  and  A. tamarii ) fungi. Aflatoxins are food-borne toxic secondary metabolites of  Aspergillus  species associated with severe hepatic carcinoma and children stuntedness. Despite the well-known public health significance of aflatoxicosis, there is a paucity of information about the prevalence, genetic diversity and population structure of  A. flavus  in different groundnut growing agro-ecological zones of Uganda. This cross-sectional study was therefore conducted to fill this knowledge gap.    Results  The overall pre- and post-harvest groundnut contamination rates with  A. flavus  were 30.0 and 39.2% respectively. Pre- and post-harvest groundnut contamination rates with  A. flavus  across AEZs were; 2.5 and 50.0%; (West Nile), 55.0 and 35.0% (Lake Kyoga Basin) and 32.5 and 32.5% (Lake Victoria Basin) respectively. There was no significant difference (χ 2  = 2,  p  = 0.157) in overall pre- and post-harvest groundnut contamination rates with  A. flavus  and similarly no significant difference (χ 2  = 6,  p  = 0.199) was observed in the pre- and post-harvest contamination of groundnut with  A. flavus  across the three AEZs. The LKB had the highest incidence of aflatoxin-producing  Aspergillus  isolates while WN had no single  Aspergillus  isolate with aflatoxin-producing potential.  Aspergillus  isolates from the pre-harvest groundnut samples had insignificantly higher incidence of aflatoxin production (χ 2  = 2.667,  p  = 0.264) than those from the post-harvest groundnut samples. Overall,  A. flavus  isolates exhibited moderate level (92%,  p  = 0.02) of genetic diversity across the three AEZs and low level (8%,  p  = 0.05) of genetic diversity within the individual AEZs. There was a weak positive correlation ( r  = 0.1241,  p  = 0.045) between genetic distance and geographic distance among  A. flavus  populations in the LKB, suggesting that genetic differentiation in the LKB population might be associated to geographic distance. A very weak positive correlation existed between genetic variation and geographic location in the entire study area ( r  = 0.01,  p  = 0.471), LVB farming system ( r  = 0.0141,  p  = 0.412) and WN farming system ( r  = 0.02,  p  = 0.478). Hierarchical clustering using the unweighted pair group method with arithmetic means (UPGMA) revealed two main clusters of genetically similar  A. flavus  isolates.    Conclusions  These findings provide evidence that genetic differentiation in  A. flavus  populations is independent of geographic distance. This information can be valuable in the development of a suitable biocontrol management strategy of aflatoxin-producing  A. flavus.

Genetic diversity of aflatoxin-producing Aspergillus flavus isolated from selected groundnut growing agro-ecological zones of Uganda