In the present work, the fungal population present in the environment and on surfaces of equipment and facilities was determined and quantified in two stone fruit packinghouses during 2012 and 2013. The fungi present in the environment were sampled according to the gravimetric method. The fungi present on the surfaces of floors, walls, containers and lines were sampled with Rodac plates. Dirty zones (reception of fruits and first selection) were more contaminated than clean zones (washing of fruits, lines and containers), even though in the shipping room the presence of different fungi was high. The most prevalent genera recovered in both packinghouses and in all zones were Penicillium spp. followed by Cladosporium spp. The presence of Rhizopus spp. was also highly detected in all zones, which could result in new postharvest infections. Moreover, Monilinia spp., the most important postharvest disease on stone fruit, was rarely detected, indicating the low risk of fruit infection in packinghouses.