Staphylococcus aureus strains which produced either high or low levels of staphylococcal enterotoxin A (SEA) with a minimal eightfold difference between the two groups were identified. For FRI100 and FRI281A (prototypes for each group), strain differences in the expression of the SEA-encoding gene (sea) were found to occur at the level of sea mRNA concentration, and part of the difference in expression was associated with the sea-containing phages. Southern blot analysis revealed that this phage-associated difference was not due to differences in the copy number of sea. Nucleotide sequence analysis of sea from FRI281A revealed a new allele of sea, with the majority of the sequence differences occurring in the upstream promoter region. Although a strict correlation was observed between the level of SEA production and sea allele class for several strains, the sequence differences observed in the upstream region were not sufficient in themselves to alter the expression level of sea.