The genome of Z. tritici encodes 1798 orphan genes (15.1% of all the predicted genes), of which 1221 are localized on core chromosomes and 577 on accessory chromosomes. However, accessory chromosomes are significantly enriched in orphan genes because they constitute 79.3% of the genes on these chromosomes compared to 10.9% on core chromosomes (χ2 test, P < 2.2e-16). A large majority of the orphan genes (95.5%) have no in silico attributed function. In general, we could not link species-specific genes to any biological or pathogenicity-related function; however, this uniqueness supports the species-specific nature of the genes that have no homology with known proteins from organisms outside the Zymoseptoria species complex. Among the orphan sequences that could be assigned a function, we found predicted functions relating to molecule transport (drugs, proteins, amino acids), primary and secondary metabolism (oxydoreductase activity, nonribosomal peptide synthase), and organic compounds degradation (chitinase, glycoside hydrolase). Small secreted proteins (SSPs) of plant pathogens particularly play an important role as putative effectors during the host infection (Stergiopoulos and De Wit 2009), and we found in Z. tritici that SSP-encoding genes were significantly enriched in the orphan gene set compared to the whole proteome: 8% vs. 3.7% (χ2 test, P < 2.2e-16). Orphan genes representing 9–11% of the predicted genes in Z. pseudotritici, Z. ardabiliae, and Z. brevis were likewise significantly enriched in SSP-encoding genes and genes that could not be assigned a function.