There is very little up to date information regarding apple microflora so in the current study we decided to address that issue and assess whether dominant fungi which reside in fruit might spoil apple juice. Microorganisms were isolated from apples of Koksa Górska harvested in the middle of October in 2016 and 2017. Identification of isolates was based on the sequencing of ribosomal DNA. Some isolates were characteristic for a particular year but in both years apple microflora was dominated by Aureobasidium pullulans. Based on phylogenetic analysis it was stated that only one isolate (LW81) was closely related to strains which are already described in available databases. All other isolates collected in the current study differed significantly from sequences stored in databases, tending to form a common cluster. It was possible to predict secondary structure of ITS2 region only for the isolate LW81, while we managed to establish the length and location of 5.8S gene in Rfam database for all sequences. A. pullulans is known exopolysaccharide producer so obtained microorganisms were tested for their ability to synthesise those substances on Czapek-Dox agar. The strain which proved to be the most significant exopolysaccharide producer (isolate LW14) was inoculated in the sterilised apple juice at three different initial cell number (100, 1000 and 10,000 cfu/ml) and subjected to pasteurisation. In all cases pasteurisation eliminated fungal growth effectively, therefore A. pullulans strains should not pose any risk to the quality of pasteurised apple juices.