Wrapped forages such as haylage and silage are increasing in popularity in equine feed rations, but knowledge of their microbial composition, especially of haylage, is scarce. Haylage may be more at risk of mould growth compared to silage, and methods for the assessment of hygienic quality of haylage are needed. Varying culturing conditions, including aerobic/anaerobic incubation, four substrates and three incubation temperatures were therefore evaluated for analysis of fungi in haylage samples from eighteen horse farms, taken on two occasions (autumn and the following spring). Average mould counts in forage samples were low, but fungi with the potential for producing mycotoxins, such as Aspergillus fumigatus and Penicillium spp., were present. The microbial composition and content of fermentation products were similar in haylage samples taken in autumn and in spring. The type of substrate used for cultivation did not influence mould or yeast counts, but not all mould species were present on all substrates. Incubation temperature influenced fungal counts and the presence of mould species. By using at least two substrates (malt extract agar and dichloran 18% glycerol agar) and two incubation temperatures (25 and 37°C), all mould species/genera that were identified in this study could be detected.