The paper provides an overview of current trends, limitations, and future research directions in the field of mycology. It highlights the significant contributions of fungi to science, technology, and industry, emphasizing their importance in medical mycology, drug discovery, and ecological studies. The authors discuss the emergence of fungal diseases, the potential of fungi in drug and novel compound discovery, and the advancements in phylogenomics and functional genomics. They also explore the role of fungi in building materials, biocircular economies, and the challenges and opportunities in fungal classification and phylogenomics. The paper addresses the need for reliable diagnostics and the development of new therapeutic approaches, particularly in the context of emerging fungal infections. Additionally, it reviews the historical development of natural product-based drug discovery from fungi and the current state of fungal drug research. The authors emphasize the importance of expanding sequencing efforts to less studied fungal groups and the integration of genomics with metabolomics and synthetic biology. Finally, they discuss the limitations and future prospects of phylogenomics in fungal taxonomy and the genomics and ecology of fungal plant pathogens, highlighting the need for increased genomic sampling and collaboration between taxonomists and bioinformaticians.The paper provides an overview of current trends, limitations, and future research directions in the field of mycology. It highlights the significant contributions of fungi to science, technology, and industry, emphasizing their importance in medical mycology, drug discovery, and ecological studies. The authors discuss the emergence of fungal diseases, the potential of fungi in drug and novel compound discovery, and the advancements in phylogenomics and functional genomics. They also explore the role of fungi in building materials, biocircular economies, and the challenges and opportunities in fungal classification and phylogenomics. The paper addresses the need for reliable diagnostics and the development of new therapeutic approaches, particularly in the context of emerging fungal infections. Additionally, it reviews the historical development of natural product-based drug discovery from fungi and the current state of fungal drug research. The authors emphasize the importance of expanding sequencing efforts to less studied fungal groups and the integration of genomics with metabolomics and synthetic biology. Finally, they discuss the limitations and future prospects of phylogenomics in fungal taxonomy and the genomics and ecology of fungal plant pathogens, highlighting the need for increased genomic sampling and collaboration between taxonomists and bioinformaticians.