Phlebiopsis gigantea strains registered in the European Union as biocontrol agents against root rot in forests (four from Great Britain and two from Finland) were compared using Ward's method with reference to: (1) similarity of DNA-random amplified microsatellite (RAMS) ladders, (2) cellulase and peroxidase production and (3) acceleration of dry mass wood loss in Norway spruce. The activity of the enzymes was tested in the initial phase of wood decay (30 d after inoculation) and indicated as the most active isolates: VF10 and FC15 for cellulase and FC16 and VF10 for peroxidase production. The assessment of loss of wood six months after inoculation indicated isolate FC15 as the most active. P. gigantea isolates similar in terms of enzyme activity indicated different patterns of DNA microsatellite loci. At the same time, DNA-RAMS revealed similarities in isolates with different abilities to produce enzymes. However, some similarities and differences between isolates according to wood decay were found. No plain relationships between molecular characteristics and enzyme activity of the strains tested were observed. The results differentiated activity of tested isolates and suggested benefits of selecting P. gigantea strains for commercial use basing mainly on the assessment of wood loss activity.