Fungi are a vital component of ecosystem biodiversity, but spend most of their lives hidden from view. Monitoring ectomycorrhizal (ECM) fungi has mostly relied on the abundance and distribution of above-ground sporocarps without consideration of their below-ground vegetative mycelium. Molecular methods may provide the means of obtaining this information and allow a more accurate determination of their possible decline and threat of extinction. Stipitate hydnoid sporocarp occurrence was recorded and mapped for 9 yr at two sites in Scotland, UK. Soil samples were collected at locations where sporocarps of Hydnellum aurantiacum, Hydnellum caeruleum, Phellodon niger or Sarcodon glaucopus had occurred 1–4 yr previously. Species-specific DNA was detected at all sporocarp locations and RNA was detected at 75 % of the locations indicating that these species remained below-ground and viable at the majority of locations for at least 4 yr in the absence of sporocarps.