Communities of Aspergillus section Flavi resident in soils planted with cotton were compared among several areas in the southern United States. Incidence of A. flavus and A. tamarii differed among areas. A. flavus incidence increased with temperature and decreased with latitude. Less than 1% of isolates were A. nomius or A. parasiticus. A. flavus isolates were assigned to either the S or L strains on the basis of sclerotial morphology. S strain isolates produced numerous small (<400 μm) sclerotia; L strain isolates produced fewer, larger sclerotia. The S strain of A. flavus was found in all areas. Aflatoxin-producing potential of A. flavus differed among areas and was correlated with S strain incidence. L strain isolates produced only 33% as much aflatoxin B1 as S strain isolates. No S strain isolate produced both aflatoxin B1 and aflatoxin G1. Correlations indicated that L strain toxigenicity but not S strain toxigenicity varied geographically. While toxigenicities of most isolates were stable through single conidial transfer, 28% of isolates expressed altered levels of toxigenicity after transfer. The observed differences among communities may reflect geographic isolation and/or adaptation, and may cause different vulnerabilities to aflatoxin contamination among crops planted in diverse locations.