Banana production is severely threatened by the Black Leaf Streak (BLS) disease caused by Mycosphaerella fijiensis. Numerous chemical applications are needed to control the fungus's impact on leaves which reduces yields and causes premature ripening of fruits. Genetic improvement for resistance to BLS disease appears as the most durable, cost and environmentally efficient control. Screening for resistance has led to the identification of two forms of resistance reported as High Resistance (HR, hypersensitive response) and Partial Resistance (PR). In connection with the breeding program, a genome mapping approach for genetic and QTL analyses was developed to characterise the HR form. An F2 segregating population of 153 plants was obtained from a cross between two wild seeded banana accessions, Musa acuminata burmannicoides type Calcutta 4 and M. a. banksii type Madang. A linkage map was constructed with 110 AFLP markers in association with 39 codominant RFLP and SSR markers to anchor the linkage groups to the banana genetic core map. Results showed significant allelic distorted segregations in the F2 progeny for 58 markers which highlight the use of molecular studies for inheritance analyses. A first mapping concluded to join the markers in 11 linkage groups. Correlations made with field observations, ranked into six classes of infection severity, led to the identification of one RFLP marker strongly associated to the resistance and a second QTL mapped onto a different linkage group with lower significance level