Stemphylium lycopersici (Pleosporales) is a pathogenic fungus found on a broad range of plant hosts. It is one of the causal agents of gray leaf spot disease in tomato that causes severe yield reductions and economic losses worldwide. Here, we present the draft genome sequences and the gene annotations of two strains of S. lycopersici, nonsporulating strain CIDEFI-212 and sporulating strain CIDEFI-213.