We revisit the phylogenetic diversity of Cenococcum geophilum (Cg) based on a partial glyceraldehyde-3-phosphate dehydrogenase (GPD) gene, by using existing data from Europe, Japan, and North American with new data from Florida. A significant amount of genetic diversity was found between continents and regions and even within individual regions such as California and Florida. Isolates from Europe and North America intermingled and some of them clustered together with high bootstrap support in the phylogenetic tree, suggesting that some lineages are ancient or have dispersed between continents. The similar pattern was also observed within North America where various genotypes of Cg inhabit a particular region whereas other lineages are widespread. On the other hand, the majority of Japanese isolates formed a single well-supported cluster distinct from Europe and North America. We discuss the phylogenetic diversity and phylogeography of Cg and potential factors that may affect the distributional patterns of Cg lineages.