Fusarium is a genus of significant concern and interest. With the development of omics technologies, sequencing and assembling fungal genomes became widely available. To date, numerous Fusarium genomes were deposited in genomic databases. This chapter highlights the importance of studying Fusarium species and discusses the structure and peculiarities of the genus Fusarium. A summary of an approach for obtaining a chromosome-level fungal genome is given, and the importance of producing a high-quality assembly is discussed. The aspects for choosing assembly software according to the sequencing data type and quality assessment tools are covered. Finally, the power of genomic analysis based on high-quality genome sequences of fungi is demonstrated.