Ascochyta blight caused by Didymella pinodes (formerly Mycosphaerella pinodes) is one of the most important fungal diseases of pea (Pisum sativum) worldwide that can also infect the model legume Medicago truncatula. The objective of this study was to identify quantitative trait loci (QTLs) controlling resistance to D. pinodes in M. truncatula. Response to D. pinodes was studied under controlled conditions in seedlings of a population derived from the cross J6 × F83005.5, two M. truncatula lines that are, respectively, resistant and susceptible to D. pinodes. A combined map using two different recombinant inbred line populations was then used to identify the genomic regions bearing putative QTLs and to improve the position of the QTLs. A single QTL associated with resistance to D. pinodes was detected on linkage group 2, explaining up to 13 % of the total phenotypic variation for relative disease severity against the pathogen. Two simple sequence repeat markers, MTE80 and mtic890 (3 cM apart) were the ones most significantly associated with the QTL. These markers are located in bacterial artifical chromosomes AC119409 and AC125474, respectively, both of them overlapping on M. truncatula chromosome 2. The integration of QTL analysis and genomics in M. truncatula will contribute to the development of new markers and facilitate the identification of candidate genes for Ascochyta blight resistance.