Seeds with high oil contents are more susceptible to aflatoxin contamination after infected by Aspergillus species. However, in vitro studies showed that different types of fatty acids have striking difference on fungal growth, sporulation and aflatoxin biosynthesis in Aspergillus. Recent studies revealed that, although all fatty acids examined promote aflatoxin production, oxidized polyunsaturated fatty acids inhibit aflatoxin biosynthesis. The inhibiting effect is derived from oxylipins produced during autoxidation. In this article, we provide an overview for recent progress in fatty acids and oxylipins on fungal growth, sporulation and aflatoxin production in Aspergillus species.