In total, we found 497 repeat families in the four Zymoseptoria species, including 120 families of class I TEs (24.1%), 135 families of class II TEs (27.2%), and 242 uncategorized families (48.7%). We could improve the TE annotation using the complete Zymoseptoria TE library generated here. We found 19.9% of repeats (+1.3%) in the genome of Z. tritici, 17.6% (+2.2%) in the genome of Z. pseudotritici, 12.7% (+4.8%) in the genome of Z. ardabiliae, and 25.2% (+1.3%) in the genome of Z. brevis.