AbstractVerticillium longisporum is a soilborne fungal vascular pathogen of Brassica crops. Three hybrid lineages originating from three independent hybridization events of four haploid Verticillium parents are known. V. longisporum lineage A1/D2 has only been found in horseradish and previous pathogenicity tests have shown that it is non‐aggressive on oilseed rape (Brassica napus). The aim of this study was to investigate the interaction of the non‐aggressive lineage A1/D2 with oilseed rape in comparison with the aggressive A1/D1 lineage. Although A1/D2 did not cause severe disease symptoms, the study revealed restricted root infection and systemic colonization by this lineage, as assessed by quantitative PCR of fungal DNA. Assessment of root surface colonization by confocal laser microscopy indicated early sporulation, disorganized loosely attached hyphal growth and hyphal coiling of A1/D2. By contrast, A1/D1 showed organized hyphal growth tight to the root surface, as well as hyphal swellings at points of penetration. Vascular colonization was studied with transmission electron microscopy, which revealed less vessel colonization, higher intensity of vascular responses and lower plant cell wall degradation in A1/D2‐treated plants in comparison with A1/D1. Vascular responses consisted of strong coating of vessel walls and fungal hyphae with an electron‐dense material, indicating higher intensity of plant defence in comparison with A1/D1. The results, for the first time, demonstrate stem colonization and thus a basic level of pathogenic interaction of non‐aggressive strains of A1/D2 with oilseed rape associated with a lack of severe disease symptoms, which indicate tolerance in oilseed rape to lineage A1/D2.