Recently, a new identification and classification of repeats and TEs in Z. tritici was conducted (Dhillon et al. 2014). In the present study we found very similar patterns in terms of repeat and TE distribution, number of families, and evidence of TE activity. However, we could further improve the assignment of repeat families to known TE families; 39.8% of the 93 repeat families identified by Dhillon et al. were not categorized into known TE classes. We were able to improve the TE classification, leaving only 9% of the 111 repeat families unclassified. The TE annotation pipeline used here contains a number of supplementary steps of clustering of the REPET outputs and allowed us to identify more complete elements. These were all manually checked to avoid the generation of false or chimera elements.