The fungal pathogen Mycosphaerella fijiensis causing black leaf streak disease of banana may be able to adapt to quantitatively resistant cultivars through changes in its aggressiveness. To understand this adaptation, it is necessary to determine the genetic basis of the aggressiveness traits involved. This study aims to identify genes of aggressiveness traits using a genome wide association study (GWAS) approach. About 130 M. Fijiensis isolates were collected on susceptible and quantitatively resistant banana trees in three different locations in Cuba. The genome of these isolates was then sequenced and SNP (single nucleotide polymorphism) calling was performed. There was low genetic structure between the three Cuban populations (Fst=0.055). Linkage disequilibrium (LD) declined to 50% within about 6kb. The population mutation rate theta first estimate was 0.06%. A phenotype study was conducted to assess some aggressiveness traits using inoculations under controlled conditions : the number of symptoms and their total surface. Based on our variance analysis, we decided to use a simplified linear model taking only the cultivar and isolate effects into account, to calculate least-square means. These preliminary analyses showed that the samples analyzed satisfy conditions to conduct a GWAS analysis (reasonable LD, limited population structure and phenotypic variability for the quantitative traits considered). Such a study is currently being performed using the GAP-IT R package.