The fungus Alternaria arborescens in a pathogen of tomato and produces AAL toxins, a group of host-specific toxins that are structurally similar to fumonisin mycotoxins. The genome sequence of A. arborescens strain NRRL 20593 will facilitate comparison of AAL toxin biosynthetic genes with fumonisin biosynthetic genes from species of Aspergillus, Fusarium and Tolypocladium.