The metabolite production of the five members of the fungal species complex Heterobasidion annosum s.l., i.e. H. annosum s.s., H. abietinum, H. parviporum, H. occidentale and H. irregulare, was analyzed by LC–HRMS. The five members are described to have differences in host preferences: H. annosum s.s. and H. irregulare are pine infecting species, and H. parviporum, H. occidentale and H. abietinum are non-pine infecting. Principal component analysis (PCA) of the LC–HRMS data showed that samples from the five species could be separated into five groups and in accordance with the differences in host preferences. Twenty-three compounds, important to the observed PCA grouping, were isolated and identified. The main contributor to the separation of the pine infecting species from the non-pine infecting species in PC1 was the benzohydrofuran fomannoxin, which was only detected in the pine infecting species H. annosum s.s. and H. irregulare. These two species were further separated in PC3, and one major contributor here was the sesquiterpene deoxyfomannosin A. The three non-pine infecting species were separated in PC2, by epoxydrimenol that was detected in only two of the species and further in PC4, where a few fomannoxin related compounds were important for the grouping. During the work, three unknown compounds were isolated and described: 3-hydroxy-2-(1,3-dihydroxypropan-2-yl)-2,3-dihydrobenzofuran-5-carbaldehyde, 3-hydroxy-2-(1,2,3-trihydroxypropan-2-yl)-2,3-dihydrobenzofuran-5-carbaldehyde and 3-hydroxy-2,3-dihydrobenzofuran-5-carboxylic acid.