A total of 34 isolates of Cylindrobasidium evolvens were obtained from wounded Picea abies in five sample plots in Sweden and Lithuania. Population structure and genetic variation within the species were assessed by somatic incompatibility and arbitrary primed DNA (AP-DNA) analysis, using the M13 core sequence as a primer. All somatic incompatibility pairings between different C. evolvens isolates resulted in weak mycelial antagonism. The AP-DNA profiles indicate genetic variation was high in the species with no differentiation among isolates being found either on a large (more than 700 km) (R2=0·108) or a fine scale (200 m) (R2=0·024). In a plot, genetic similarity was significantly higher (P<0·02) among isolates from wounds infected during the previous 2 years than among the rest of the same population.