These mycological investigations are implicating samples of protein sunflower seed from regular cultivation in the Vojvodina Province. Samples are examined in different stages of production: reception in the silo, separation of massive fraction on peeler and then peeling, kernel after peeling, hull, final product, i.e. kernels separated from visible impurities on conveyor bel, that are later manually divided in two fractions - a) seemingly whole, undamaged kernels, without change of colour, and b) seemingly damaged kernels, broken, with change of colour. For the determination of viable count of moulds and their isolation, two different media are used in parallel: Sabouraud maltose agar (SMA) and malt/yeast extract with 50% of glucose (MY50G), favourable for growth of xerophilic moulds. All samples tested were contaminated with fungi. Total viable mould count per seed varied from 1.6 (SMA) respecting 1.3 (MY50G) on reception, to 5.6 (SMA) and 7.5 (MY50G) cfu/seed in visually damaged sunflower kernels (final product). From seeds, kernels and hull, numerous moulds were isolated, belonging to 8 genera and 13 species (Alternaria alternata, Arthrinium phaeospermum, Aspergillus candidus, A. flavus, A. niger, A. ochraceus, A. versicolor, A. wentii, Cladosporium cladosporioides, Eurotium herbariorum, Penicillium aurantiogriseum, Rhizopus stolonifer and Trichoderma harzianum). Alternaria alternata, Aspergillus flavus, A.ochraceus, A. versicolor and Eurotium herbariorum were isolated on both media. Aspergillus candidus, A. versicolor, C. Cladosporioides, P. aurantiogriseum and T. harzianum were isolated only on SMA, while A. niger, A. wentii and R. stolonifer were exclusively isolated on MY50G. Most ubiquitous species is A. alternata, which is isolated from all tested samples, while A. candidus, C. cladosporioides and T. harzianum were isolated from sunflower seed on reception in silo, using SMA medium