Variation in Gremmeniella abietina var. abietina was studied in three stands of Scots pine in northern Finland and in the Kola Peninsula. Eighty-four isolates of large- and small-tree types of G. abietina var. abietina (LTT and STT, respectively) were identified on the basis of tentative characteristics (spore morphology, disease type and host size), fatty acid and sterol profiles (FAST), and random amplified microsatellite technique (RAMS). Both LTT and STT occurred in all three stands. In general, the classifications obtained using the three methods agreed with one another, although a few contradicting results were observed. Variation in fatty acids and sterols in G. abietina var. abietina was rather low, although the amounts of some individual extractives showed statistically significant differences between the stands. All pathogenic and asymptotic G. abietina var. abietina isolates originating from branches located at heights above the annual snow cover were identified as LTT based on RAMS, but some were grouped to STT according to their FAST profiles. Both STT and LTT were detected among the isolates obtained from seedlings according to both FAST and RAMS. In addition, in two cases RAMS markers thought to be STT- or LTT-specific were found in the same isolate. The results presented here suggest that LTT of G. abietina var. abietina caused the devastating epidemics on pines in the first-thinning stage or middle age similar to pines in this study reported in northern Finland and in the Kola Peninsula during the 1980s.