An ultrastructural investigation on the infection of susceptible and tolerant lines of sunflower (Helianthus annuus L) using artificial inoculation with Phoma macdonaldii Boerema conidiospores was carried out using scanning, transmission electron microscopy, and light microscopy to elucidate the host-parasite relationship. Results revealed the occurrence of direct penetration through the cuticle of cotyledon, petiole and roots after adhesion to the plant surface without prior formation of appressoria. Mechanical penetration of cell walls by the fungal hyphae was demonstrated, and no enzymatic degradation at the penetration point was observed. The evolution and progression of the fungus within stem and root tissues after penetration differed according to host susceptibility. The pathogen has similar morphological features in different root tissues of the susceptible genotype roots. In contrast, differences in morphological features of hypha based on location of the pathogen in root tissues was noted in the tolerant genotype. The pathogen was observed only in the roots cortex of tolerant line, and could not proceed further, with the presence of many empty hyphae. Whereas the whole root tissues including the vessels of susceptible line were colonized by the pathogen with only few empty hyphae.