ABSTRACT Ectomycorrhizal fungi (EMF) are critical to the establishment of many plant species and an important consideration in ecological restoration of southern beech (Nothofagaceae) forest. However, information on spore viability and storage is lacking for EMF taxa associated with southern beech. This study tested the viability and germination of spores from fruiting bodies collected during autumn and spring from mountain beech forest, Otago, New Zealand. Nuclear ribosomal ITS sequences matched autumn collections to the EMF genera Cortinarius, Inocybe and Russula, but all spring collections were an undescribed hypogeous taxon resembling the native EMF genus Hysterangium, referred to here as Hysterangiaceae ‘Motatapu’. We investigated propidium iodide as a spore viability test, and compared spore germination in water vs glucose, in different temperature and light regimes, and between freshly collected spores and spores from fruiting bodies dried at 30°C or frozen at −20°C. Propidium iodide did not stain all devitalised spores, so may be unreliable for quantifying viability of fresh spores. Spore germination in water was <6% for all genera and <2% for most taxon × treatment combinations. Fresh spores of Hysterangiaceae ‘Motatapu’ suspended in 4°C water showed higher germination than at 20°C; excluding light had no significant effect. Spores of the same taxon suspended in 10% and 20% glucose showed lower germination in comparison to water and showed deformations. Germination percentages of all taxa decreased with storage, but spores of some taxa retained viability for 120 days in 4°C water suspensions. Spores of Hysterangiaceae ‘Motatapu’ showed the least loss of viability with storage of all taxa investigated. For the purposes of storing EMF material for use as inoculum, we recommend drying fruiting bodies at 30°C for storage, then preparing fresh spore suspensions in water when inoculum is required.