Mycetoma is a neglected tropical disease, characterized by slowly evolving tumorous subcutaneous masses containing either bacteria (e.g., Actinomycetoma) or fungi (e.g., Eumycetoma; Madura foot). The fungal agents of mycetoma, including several genera belonging to the Pleosporales order of Ascomycetes, were designated high-priority pathogens in the WHO Fungal Priority Pathogens List of 2023 to signal the need for additional research and development and public health action. Despite this, many of the fungal causative agents are poorly described, especially in terms of the genomic basis for disease, their epidemiology, and evolutionary history. Recently, the new genus Emarellia was described, including two sister species, E. grisea and E. paragrisea. To gain insights into the virulence and/or pathogenicity features of eumycetoma, we describe the first genome assembly and gene annotation for Emarellia grisea and compare this genome assembly to those currently available for other agents of eumycetoma and close relatives, Madurella mycetomatis and Trematosphaeria pertusa. We also describe the gene annotation for the genome assembly of Nigrograna (formerly Biatriospora) mackinnonii, which hitherto lacked annotation. Our genome assembly comprises 691 contigs representing 28.23 Mb of sequence, with very low repeat content. Genes uniquely encoded by E. grisea included an enrichment of secretion signals, suggesting possible new virulence factors. We also found that E. grisea produces a diverse array of endo- and exopeptidases, which may contribute to its virulence and drug resistance. We anticipate that our genomic resource and analysis will benefit future studies on the genomic basis for pathogenicity in neglected fungal agents causing eumycetoma or similar subcutaneous lesions in humans.