AbstractThe influence of fungi on seedling emergence of naked and hulled spelt (Triticum spelta L.) and winter wheat (Triticum aestivum L.) was investigated. Seeds were sown in flat trays and placed in a growth chamber under stress conditions (low temperature and water logging) for four weeks, followed by favourable growth conditions. At weekly intervals, 150 seeds were removed, surface sterilized, and investigated for fungi. Pythium aristosporum Vanterpool, a causal agent of damping‐off, was found to be best adapted to the unfavourable conditions and to be a major cause of pre‐emergence damping‐off. The frequency of seed‐borne fungi decreased during the stress period, whereas soil‐borne fungi survived and could be isolated from seeds and glumes in the following period with more favourable growth conditions. Seedlings from hulled seeds of spelt emerged more frequently than from naked kernels of spelt and both emerged at a higher rate than from seeds of winter wheat. This is good evidence that glumes protect seeds against fungal colonization and therefore increase the fitness of spelt under unfavourable germinating conditions.