Genetic diversity at 10 loci encoding six enzymes was studied in 17 European populations of Sorbus aucuparia L. (the rowan), distributed among five regions, from Finland to the Pyrenees. Levels of genetic diversity were high both at the species level (He = 0.229) and within populations (mean He = 0.212), whereas levels of differentiation among populations were very low (GST = 0.060). These values were comparable to those observed in other woody species with similar ecological traits. Populations from the Plateau des Tailles (Belgium) exhibited an unexpectedly high level of differentiation among populations, which was tentatively explained by the recent history of colonization experienced by these populations. Despite the low overall differentiation, geographical patterns were observed. Gene flow estimates and geographical distances between pairs of populations appeared to be correlated (r = −0.483), resulting in a pattern of isolation by distance, which was disrupted to some extent by the local dynamics of the Tailles populations. Cluster analysis revealed that populations were genetically more similar to populations from the same region compared to populations from other geographical groups. Finnish populations, in particular, appeared to be highly differentiated from more southerly populations.