Mycosphaerella fijiensis (anamorph: Paracercospora fijiensis) is a hemibiotrophic fungal pathogen of banana and the causal agent of the devastating Black Sigatoka or black leaf streak disease. Its control frequently requires weekly fungicide applications when bananas are grown under disease-conducive conditions, which mostly represent precarious tropical environments. We started a multidisciplinary research program on M. fijiensis that is aiming at pesticide reduction. The first goal was to collect genomic data and to develop tools for molecular analysis of this pathosystem. These included the identification of the electrophoretic karyotype, construction of a high quality genetic linkage map and the sequencing of the entire genome. Here we review the current status of these approaches.