The study aimed at being a mycological evaluation of spring barley grain harvested from the barley-pea intercrop, on which different methods of weed control had been used. The field experiment was carried out during 2010-12 and it was conducted using randomized block design in four replicates. Weed control was mechanical (spring-tine harrow treatment of variable intensity) and chemical (herbicide Chwastox Extra 300 SL – 3L per ha). Fungal colonization tests were carried out on disinfected and non-disinfected grains. The research has shown statistically significant differences in the total number of fungi isolated from disinfected and non-disinfected grains in particular years of study, between the objects, and in some cases between the study years. The fungus most frequently isolated from all variants of the experiment was Alternaria alternata. Penicillium chrysogenum was isolated only from non-disinfected grains. Presented results show that mechanical weed control treatments of appropriately adjusted intensity do not increase fungal colonization of barley grains in mixed culture with peas, as compared to the herbicidal control. The best variant of mechanical weed control for the cereal-legume mixture in terms of mycological quality of barley grain was one passage of spring-tine harrow at full tillering stage of barley. Mechanical weed control may be an alternative to herbicides in weed control in cereal-legume mixtures and may be particularly important for organic and integrated farming.