Many plant pathogenic fungi are the subject of intense study because they cause disease symptoms that have a severe negative effect on the yield or quality of tomatoes (Lycopersicum esculentum M.) and its products. The common fungi associated with tomatoes and tomato pastes were determined and compared to get information on whether the mould content of the tomato pastes originate entirely from the tomato or from the soil. Eighteen species which belong to 7 fungal genera (Alternaria, Aspergillus, Fusarium, Mucor, Penicillium, Rhizopus and Trichoderma) among 250 mould isolates were determined of tomatoes and home-made tomato pastes collected from Manisa Province and its surrounding (Turkey). Alternaria alternata was the most prevalent fungal species. Members of Aspergillus niger group represent 1/6th of all the identified species. Seven of the species are the types of species that may potentially produce mycotoxins.