Background and rationale: Histoplasma capsulatum (H. capsulatum) is a saprophytic fungal which is dimorphic in nature and strive beautifully in soil rich in nitrogen. Inhaling of infectious spores by mammalian species can result to an infection which can be localized in the lungs infection or disseminated histoplasmosis. Method: Genomic DNA was extracted from the yeast cells with Pure gene DNA isolation kit and quantified by Nano drop technology. Conventional PCR procedure was used to amplify the ITS regions of H. capsulatum and primers (ITS1 and ITS2) used were based on the ITS sequence of H. capsulatum, deposited in the Gen Bank (accession number U18363), while Sequencing of the internal transcribed spacer (ITS) of the 16S rRNA genes of the H. capsulatum were examined for the nucleotide sequences of ITS1, the 5.8S rRNA gene, and ITS2 region. This was to determine the Sequence variations in both ITS regions which allowed the exploration of the diversity of H. capsulatum in the study area and to study the Phylogenies / epidemiology of the fungus. Result: Maximum likelihood and close relationship analysis was used to identify strains that fall under geographical clades that have been widely identified in literature. In our study, we were able to have isolates identifying with Eurasian clades (China 5.6 %; Spain 22.2 % and Malaysia 27.8 %) and Netherland Clade (5.6 %). Conclusion: All our isolates identified in this study are origin of African as literature had it that Histoplasma capsulatum variety duboisii is associated with African continent.