In the study of human pathogens most of the attention has been given to viral and bacterial species, and fungi have been largely neglected. To date there is no broad, large-scale census of the genomic elements shared by fungal pathogenic species. Also, no large-scale scan for selective pressure variability has been undertaken, even though all the elements are in place to do so. There has neither been a multi-species search for conserved noncoding elements that may be key to explaining the regulation of crucially important functional elements and networks. The overall goal of this study is to gain insight on the evolution of the genomic elements involved in fungal human pathogenicity through the analysis of the selective constraints acting on coding and noncoding sequences. For this purpose we will combine genome sequencing, transcriptomics (RNA-seq), comparative genomics and evolutionary analyses. This project will throw light on fundamental questions about the key genes, regulatory elements and phenotypic traits that are involved in infection or how emergent, opportunistic pathogens originate relatively rapidly from non-pathogenic ancestors. Finally, the list of identified relevant genes and regulatory elements can provide much needed targets for developing pharmaceutical and therapeutic strategies.