Plant pathogenic fungi are able to erode quantitative host resistance through changes in aggressiveness, thereby threatening the durability of host resistance. Such erosions are suspected in some areas in the fungus Mycosphaerella fijiensis, responsible for a recent and devastating banana pandemic, Black Leaf Streak Disease (BLSD). This study aims to test for the action of host-specific adaptation and to detect host-selected genes in M. fijiensis. We collected six samples in Cuba in three locations distributed throughout the banana production zones where resistant cultivars have been used for about 15 years. For each location, about 40 isolates were collected from two banana plots containing either a resistant variety or a susceptible variety located two to 10 km apart. We also included in the study three samples from Honduras where the disease was first introduced in the Latin America- Caribbean area. Some aggressiveness traits of a subsample of about 100 Cuban isolates coming from the three locations and the two cultivars were evaluated under controlled conditions on the same cultivars. A significant host effect was detected in some locations. A genome scan approach was conducted from whole-genome sequencing of pools of individuals (pool-seq). Differentiated genomic regions were detected between pathogen populations from the two cultivars in some locations. Further analyses have been undertaken to elucidate if these differentiated regions are due to either a host selective effect or demographic history.