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The Pezizomycotina, commonly known as the filamentous fungi, are a diverse group of organisms that have a major impact on human life. The filamentous fungi diverged from a common ancestor approximately 200 – 700 million years ago. Because of the diversity and the wealth of biological and genomic tools for the filamentous fungi it is possible to track the evolutionary history of genes and gene networks in these organisms. In this dissertation I focus on the evolution of two genes (lolC and lolD) in the LOL secondary metabolite gene cluster in Epichloë and Neotyphodium genera, the evolution of the MAP kinase-signaling cascade in the filamentous fungi, the regulation of the gene networks involved in asexual development in Neurospora crassa, and the identification of two genes in the N. crassa asexual development gene network, acon-2 and acon-3. I find that lolC and lolD originated as an ancient duplication in the ancestor of the filamentous fungi, which were later recruited in the LOL gene cluster in the fungal endophyte lineage. In the MAP kinase-signaling cascade, I find that the MAPK component is the most central gene in the gene network. I also find that the MAPK signaling cascade originated as three copies in the ancestor to eukaryotes, an arrangement that is maintained in filamentous fungi. My observations of gene expression profiling during N. crassa asexual development show tissue specific expression of genes. Both the vegetative mycelium and the aerial hyphae contribute to the formation of macroconidiophores. Also, with the help of genomic tools recently developed by researchers in the filamentous fungal community, I identified NCU00478 and NCU07617 as the genes with mutations responsible for two aconidial strains of N. crassa, acon-2 and acon-3 respectively.