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Histoplasmosis is one of the most under-diagnosed and under-reported endemic mycoses in the United States. <i>Histoplasma capsulatum</i> is the causative agent of this disease. To date, molecular epidemiologic studies detailing the phylogeographic structure of <i>H. capsulatum</i> in the United States have been limited. We conducted genomic sequencing using isolates from histoplasmosis cases reported in the United States. We identified North American Clade 2 (NAm2) as the most prevalent clade in the country. Despite high intra-clade diversity, isolates from Minnesota and Michigan cases were predominately clustered by state. Future work incorporating environmental sampling and veterinary surveillance may further elucidate the molecular epidemiology of <i>H. capsulatum</i> in the United States and how genomic sequencing can be applied to the surveillance and outbreak investigation of histoplasmosis.