The phylogeny of the vertebrate pathogen Histoplasma capsulatum and its varieties was analyzed on the basis of GenBank data, comparing preceding papers that distinguished lineages on the basis of a much smaller dataset, partly dating back two decades. The aim was to establish the predictive value of individual research papers on biodiversity, which eventually may lead to altered nomenclature with large clinical consequences. A total of 1985 sequences of ITS, ARF, OLE and H-anti were downloaded. ITS showed insufficient resolution, and the sequences of the H-anti gene were too short to provide reliable conclusions. Ten major lineages from the seven reports were selected for comparison. Compared to the currently available global data, several earlier studies applied somewhat skewed datasets, biased towards the Americas. Possible separation of Indian and Indonesian lineages were consequently overlooked. Previously distinguished lineages were again recognized, but because of low bootstrap values and extensive genetic exchange, several of these do not deserve species status. No recombination was observed with North American H. mississippiense and H. ohiense. An African clade (var. duboisii) was individualized. Despite its position in close association with South American clades, histopathology and clinical course of this entity underlines that it has other evolutionary drivers. This might also hold true for the North African donkey disease caused by var. farciminosum, although strains analyzed thus far are indistinguishable from South American strains. On the basis of phylogenetic data, Indian and Indonesian clades are separate, but more clinical data are needed to establish their value as individual species.