Leptosphaeria maculans, the fungal pathogen of Brassica napus, is the causal agent of Blackleg disease, the most devastating disease of B. napus worldwide. L. biglobosa is a closely related species which also causes yield losses to B. napus in Europe and can be found growing on the same plants at the same time as L. maculans. Although both fungi enter the leaves of B. napus through wounds or stomatal openings, L. biglobosa causes a rapid necrotic lesion whereas L. maculans grows asymptomatically in the leaf before the onset of necrosis and only L. maculans forms necrotic stem cankers. The metabolites produced by these two fungi are relatively unknown apart from the secondary metabolites sirodesmin PL and phomenoic acid which are made only by L. maculans. In order to further define the role of sirodesmin during infection of canola stems, a comparison of metabolites made by the wild type and sirodesmin mutant isolates during growth in canola stems was made. Infected tissue was either ground and extracted with ethyl acetate and metabolites detected by liquid chromatography/mass spectrometry (LC-MS) or stems were sectioned and fixed to a slide whereupon metabolites were visualised using matrix–assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI). Identical techniques were used to compare metabolites made by wild type and sirodesmin mutant isolates while grown on agar plates in isolation or adjacent to a competing L. biglobosa colony. Sirodesmin was localised in infected stem canker tissue and was also found to be upregulated in the presence of L. biglobosa. This is the first time an untargeted metabolite profile has been generated for Leptosphaeria species during growth in planta and in culture and may lead to identification of novel compounds important for the interaction of L. maculans with its host and competitors.