Studying fungal diversity in various environmental samples provides us with valuable knowledge about the occurrence of fungi of medical and ecological importance. Moreover, fungal composition may also characterise well the botanical and geographical source of food products, such as the origin of the spore enriched honeydew honeys. Thereby, we identified a wide spectrum of fungi found in 100 of honey samples from various geographical sources – most of them were from Italy, Greece and Hungary. Our honeydew honeys had a higher mean of the number of spore types found in them than floral honeys had. Statistically significant differences in diversity were found regarding the botanical source (p = 1.29 × 10–9) and the climatic classification (p = 2.28 × 10–2) according to Kruskal– Wallis rank sum tests. Most frequently encountered genera included ubiquitous saprotrophic species (Alternaria, Cladosporium, Epicoccum nigrum, Stemphylium), both in floral and honeydew honeys. On the other hand, certain sooty moulds like Aureobasidium pullulans, Tripospermum and Capnobotrys were rather present in different types of honeydew honeys. Metschnikowia reukaufii, the nectar inhabiting yeast reached considerably high quantities in floral honey samples. Present findings encourage further studies on quantifying the occurrence and the indicator value of specific fungal elements in honey, concerning its origin.