Two genetically related strains of Tuber borchii Vittad. (1BO and 43BO) produce mycorrhizas with Tilia platyphyllos Scop. with a different degree of efficiency. The aim of this work was to characterize the morphology of the fungal symbiotic structures in order to examine potential relationships between the anatomical traits of the mycorrhiza, the mycorrhizal capacities of the fungal strains and their effect on the host plants. Some morphological features of mantle hyphae (small size, intense staining, vacuolization, abundance of mitochondria) led to a mantle with morphological features that were isolate-specific. There were unexpected differences, at least under our experimental conditions: 1BO strain mantle cells were larger, less reactive to staining, more highly vacuolated and poorer in mitochondria than those of 43BO. These features were found throughout the mantle in 1BO, while the inner mantle hyphae of 43BO were significantly smaller and more intensely stained than the outer cells. In the 43BO strain there was a positive relation between these features and higher infectivity (evaluated as percentage of mycorrhizal tips) as well as a slightly more effective stimulation of plant growth. These observations suggest that genetically related truffle strains produce mycorrhizas with different morphologies, which may be related to a more efficient response of the host plant to inoculation.