Our study was a mycological evaluation of pea seeds harvested from a barley-pea mixture in which different methods of weed control had been used. The field experiment was carried out during 2010-12 and was conducted using randomized block design in four replicates. Weed control was mechanical and chemical. Fungal colonization tests were carried out on disinfected and non-disinfected seeds. The research showed statistically significant differences in the total number of fungi isolated from disinfected and non-disinfected seeds. The fungus most frequently isolated was Alternaria alternata. Penicillium chrysogenum, Sclerotinia sclerotiorum, and Trichoderma harzianum were isolated only from the non-disinfected seeds. Presented results show that suitably chosen mechanical weed control may be an alternative to chemical weed control in the mixtures of cereals and legumes, and may be particularly important for organic and integrated farming. The best variant of mechanical weed control in the cereal-legume mixture in terms of infection pea seeds by fungi is two passes of spring-tine harrow at the beginning of the tillering stage of barley and two passes at the full tillering stage of barley.