Apricot fruit is highly susceptible to infection by pathogenic fungi. In this study, the pathogenic fungi in the diseased parts of the fruits of ‘Golden Sun’ and ‘Red almond’ apricot (Prunus armeniaca L.) during postharvest storage were isolated and purified, and the purified strains were inoculated back to the healthy fruits of corresponding varieties, showing the same disease symptoms as the diseased fruits. Five fungi isolates were identified based on morphological characteristics and internal transcribed spacer (ITS) sequence analysis combined with construction of phylogenetic tree. Three isolates from ‘Golden Sun’ apricot were identified as Diaporthe eres (325#), Botryosphaeria dothidea (327#) and Aureobasidium pullulans (328#). Two isolates from ‘Red almond’ apricot were identified as Botrytis elliptica (326#) and Botrytis cinerea (331#). D. eres, B. dothidea, A. pullulans and B. elliptica were pathogenic fungi that had not been reported in the literature on apricot fruits, whereas B. cinerea had not been reported on the infection of ‘Red almond’ apricot. The present results provided references for the biological control measures of apricot fruits.