Zymoseptoria tritici is a necrotrophic pathogen of wheat, with a long asymptomatic period, followed by extensive plant necrosis and active pathogen growth. The mechanisms through which the fungus rapidly induces host cell death remain largely unknown and is currently hypothesized to be mediated by the secretion of small proteins or metabolites. These molecules are commonly referred to in fungal pathogens as effectors. This work seeks to exploit variation at the genomic level on a differential set of 13 isolates known to vary in virulence towards a range of Australian wheat cultivars in order to identify effector gene candidates. We use whole genome re-sequencing to identify single nucleotide polymorphisms and probable presence/absence polymorphisms in coding regions throughout the genome. This analysis has identified over 1 million SNPs and over 3,000 putative gene absences in at least one of the 13 genomes. The rate of gene absence is significantly higher on Z. tritici's eight accessory chromosomes when compared to the 13 core chromosomes.We have developed a python tool, PhyBi, which rapidly sorts through gene trees in order to match genotypic variation with known virulence phenotypes.