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A collection of 103 fungal strains was established from infected common bean plants (Phaseolus vulgaris L.) field-grown in three geographic regions from Tunisia and known for their long history in bean culture; Boucharray, Chatt-Mariem, and Metline. The fungal strain collection was established from common bean root and aerial parts. The pathogenicity test carried out on germinated seedlings showed that among the fungal collection, 41% of fungal strains were assigned to be highly pathogenic. In fact, serious cases of seedling damping-off, as well as a significant reduction in root and shoot biomass in cv. Coco blanc were noticed (up to 90% biomass reduction) considering fungal strains from the three prospected localities. The identification of fungal isolates belonging to this high pathogenicity class, based on the internal transcribed spacer region (ITS), showed a wide generic and specific diversity among common bean pathogenic fungi in Tunisia. Fusarium spp. strains were dominant and represented 67% of the characterized fungal collection. Fungal genera including Alternaria (22%), Rhizoctonia (4%), Ascomycota (4%), Macrophomina (10%) and Phoma (4%) were also reported. The highest richness levels were found in the Chatt-Mariem and Boucharray regions, showing the highest generic and interspecific diversity. In this work, we revealed also a variability in the abundance and geographic distribution of fungal species between the three prospected regions. Fungal strains infecting common bean in Metline were represented exclusively by Fusarium oxysporum. However, the genus Fusarium represented about 66% of fungal strains recovered from Boucharray, and only 20% from Chatt-Mariem. The genus Alternaria represented 11% and 40% of total fungal isolates in Boucharray and Chatt-Mariem, respectively, and was isolated only from the foliar parts of diseased common bean plants. The present work represents an important database that should be considered for surveying common bean fungal diseases.