Abstract: Blue mold, caused by Penicillium expansum is one of the most important postharvest diseases of apple fruit worldwide. Disease can cause significant economic losses during storage, as well as losses of processed food commodities due to the production of mycotoxin patulin. Incidence of pathogens associated with postharvest fruit rots in Croatia was surveyed during two storage seasons (2009/2010 and 2010/2011) in Ultra Low Oxygen (ULO) conditions and conventional atmosphere (NA). Diseased fruit (cultivars Idared, Jonagold, Golden Delicious and Cripps Pink) with blue mold symptoms were collected and 36 Penicillium isolates were recovered. Identification was based on macroscopic and microscopic features on different media. Molecular identification was based on PCR with primer pair PEF/PER for specific detection of P. expansum. Based on morphological and molecular methods P. expansum was detected as causal agent of blue mold of apples in Croatia. P. expansum was the predominant pathogen of decayed fruit, accounting for averages of 39.0 and 27.9% on Idared in both seasons and 37.5% on Jonagold in 2009/2010. On the other hand, during storage in NA yield losses were higher, P. expansum was detected as minor pathogen, accounting for 2.3 and 3.7%, while brown rot (Monilinia fructigena) was prevalent disease. It can be concluded that storage conditions impact pathogens and losses they cause. Since in Croatia, only products containing fungicides boscalid and pyraclostrobin are registered for control of postharvest diseases of apple, new methods such as heat treatments, biological control etc. should be implemented in apple production to prevent fungal diseases and postharvest losses.