Heterobasidion spp. pathogenic fungi produce conspicuous fruitbodies on infected wood, which may represent a habitat for a range of organisms, including invertebrates. The aim was to: (i) assess and compare invertebrate diversity in Heterobasidion spp. fruitbodies, infected Picea abies wood and adjacent soil; (ii) test methods for collecting invertebrates from Heterobasidion spp. fruitbodies. A total of 69 Heterobasidion fruitbody samples, 46 wood samples and 19 soil samples were collected at two forest sites in Latvia. In total, 7311 invertebrate individuals were collected representing 62 different taxa, among which 55 were in fruitbodies, 47 in wood and 36 in soil. The dominant invertebrates in fruitbodies were Acari (82.4%), Collembola (6.2%), Coleoptera (4.7%); in wood were Acari (78.6%), Collembola (9.6%), Diplopoda (3.1%); in soil were Acari (90.6%), Collembola (3.4%) and Coleoptera (1.4%). Among all taxa, 17.7% were found exclusively in fruitbodies, 3.2% in wood, 4.8% in soil, while 48.4% were shared among different substrates. Although many invertebrate taxa were shared, their relative abundance differed substantially among different substrates. The sampling methods used provided valuable information on invertebrate communities. Further development of these methods may be needed to obtain more detailed and specific information about invertebrates inhabiting different habitats.