Sooty blotch is one of the most common disease of apples in organic orchards in many countries. Results of molecular studies performed in USA indicated approximately 30 different fungi species associated with this disease. Fungi species causing sooty blotch in Northern, Central and Eastern Poland were identified on the basis of morphology and nucleotide sequence of the rDNA internal transcribed spacer region (ITS). A total 245 isolates were collected in spring and early summer in the years 2006–2009 from fruits with visible symptoms of the disease. Isolates were grown on PDA medium and identified on the basis of morphological characters. DNA was extracted from representative isolates and used as matrices for PCR amplification with ITS1F and ITS4 primers. Fragments of amplified rDNA ITS were sequenced. It was found that 66.53% of all isolates causing sooty blotch were species from genera Microcyclosporella, followed by Aureobasidium pullulans – 22.86%, Microcyclospora sp. –6.12%, Phialophora sessilis – 3.67%, Peltaster sp. and P. fructicola – 0.41%.

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