Monilinia fructicola, causal agent of brown rot of stone fruits, is an economically important problem worldwide. Six of the sequence tagged microsatellite sites developed for M. fructicola were used to genotype 68 M. fructicola isolates, which included isolates from three cities in Turkey (n = 42) that were compared to isolates from the USA (n = 15) and Italy (n = 11). AMOVA indicated a significant differentiation among samples from the three different countries. Samples from Turkey represented with nine haplotypes indicating a low diversity according to these markers. Samples from the USA with 12 haplotypes showed the highest genetic diversity values among the sample group from the three countries. However, all the samples from Italy were found as a single haplotype with those markers. Based on Nei's genetic distance measurements, the single genotype from Italy was distinct from the others and samples from Turkey and the USA were genetically closer to each other, which also presented on the principal coordinate plot. While informative, these results suggest that ascertainment bias in marker development may limit the power of these markers when applied to populations of M. fructicola from other locations in the world. Knowledge on genetic diversities and comparative analysis provides valuable insight for recent changes and movements in pathogen populations which is important for the disease management.