Technical Abstract: Knowing the genetic diversity of plant pathogenic fungi is essential in the management of crops and disease. The genetic variability of fungal pathogens can be evaluated using molecular markers, among which, microsatellites are a relatively inexpensive source of information. We have developed an efficient method to isolate microsatellites of organisms from which no genome sequence is available. We have also adapted this method to high throughput sequencing in order to generate a large number of markers for genetic mapping. We have shown the use of these markers in developing hypotheses to explain host-pathogen interactions. We will discuss the development and use of microsatellite markers for three plant pathogenic fungi, Macrophomina phaseolina, Cercospora sojina and Puccinia kuehnii.