Phyllosticta capitalensis Hennings is a broad-host-ranging cosmopolitan endophytic fungus. Since the description of P. capitalensis by Hennings in 1908, its geographical origin and dispersal route are still unknown. This study performed a population genetic analysis to understand the phylogeographic distribution of P. capitalensis. We examined the six populations of this fungus from three different geographical and climatic zones: tropical (Indonesia), subtropical (Okinawa, Japan), and warm temperate (the main Is. of Japan) regions. The population genetic analysis was performed based on the rDNA ITS regions of 597 base pairs and 34 polymorphic sites of 370 endophytic P. capitalensis sequences, and then 30 haplotypes were found. A total of 30 haplotypes were detected with 0.58655 haplotype diversity (Hd) and 0.00264 nucleotide diversity (Pi). The number of haplotype was higher in two Indonesian populations: 17 haplotypes and 12 haplotypes and the less from two populations that come from subtropical and warm temperate regions with 3 haplotypes. The major haplotype is Hap 2 (63.5%), followed by Hap 1, Hap 15, and Hap 13, 6.2%, 5.6%, and 4.0%, respectively. The phylogeny network partially revealed star-like shape and the Hap 2 was centered among the haplotypes. Hap 9 and 10 were detected only in two subtropical islands in Okinawa. Moreover, several haplotypes were specific to the warm temperate region in Japan, and some of them were genetically diverged. These results suggested a complicated evolution history with rapid radiation. Hap 2 probably originated in tropical region and the local diversification in subtropical and warm temperate regions.