In recent years, apple core rot have frequently been observed in East and West Azarbaijan provinces, Iran. As apple plays a major role in food industry, in present study fungal groups involved in apple core rot disease were elucidated by means of morphology and DNA sequence data. Apple fruits were purchased from local market in Tabriz, Khoy, Shabestar, Sofiyan, Talesh, Miyandoab and Jolfa cities. Small pieces from core tissues of apple fruits were surface-sterilized and plated on malt extract agar medium. Isolated fungi were purified and then identified using morphological and DNA sequence data. For molecular evaluation, DNA extraction carried out on pure cultures of selected fungal isolates and ITS region of ribosomal DNA (ITS-rDNA) was amplified and sequenced. In total, from the 30 isolates evaluated in this study, Alternaria and Penicillium species with 13 and 9 isolates were the most prevalent fungal groups. The other fungal groups were identified as Cladosporium spp. Tricothecium sp., Acremonium sp. and Stemphylium sp. Most of the fungal groups isolated in this study are toxicogenic; however, the main focus has been on the mycotoxin produced by Penicillium and Aspergillus in apple products, so far. The results of this study urge awareness on the possible contamination of apple fruit and its products by Alternaria toxins.