Aspergillus flavus, the causal agent of aflatoxin contamination, is a natural inhabitant of soils. A. flavus can be divided into two strains, S and L, with S strain isolates having a greater aflatoxin contamination potential than L strain isolates. Aflatoxin contamination can be severe in several crops in South Texas including cottonseed and corn. A. flavus communities in soils of South Texas cropped to cotton, corn and sorghum were studied to determine if crop rotation influences the magnitude and composition of A. flavus communities. On average, propagules/g was higher in fields where the previous crop was corn compared to either cotton or sorghum. On the other hand, fields in South Texas previously cropped with cotton had more S strain than fields previously cropped with corn. Fields previously cropped to sorghum were intermediate between those cropped to cotton and corn. Thus, in South Texas, crop rotations influence both the quantity of A. flavus in soils and the average of aflatoxin producing potential of Aspergillus communities.