Abstract A number of willow clones are today in use in short rotation intensive culture plantations. The clonal nature of this crop makes it an easy target for pests and pathogens when grown in monocultures. This is a major concern as plantations of coppice must remain viable for up to 20 years to be profitable. In this paper the genetic diversity of 114 selected willow clones was examined and the possible solution of growing willows in multiclonal plantations is discussed. Forty five Salix eriocephala clones, 53 S. exigua clones and 16 clones of their inter-specific hybrid (12 S. eriocephala × exigua clones and 4 S. exigua × eriocephala clones), were evaluated. Starch gel electrophoresis was employed and 12 enzyme systems were used for the assessment of the genetic variation in the clonal material. A total of 29 loci and 57 alleles were revealed. Three measures of genetic diversity were used in order to evaluate the genetic base of the clonal set: average number of alleles per locus, percentage of polymorphic loci and mean heterozygosity. Results indicated that the genetic diversity within a species, is generally lower than the genetic diversity observed in natural populations or full-sib families of the same species. These results, however, are within the limits obtained from natural populations of the Salicaceae family. Heterozygosity values were found to be greater than similar values from poplar clonal material. In contrast to the results within species, inter-specific hybrid clones presented relatively high amounts of genetic diversity. The significance of these results in the management of clonal plantations is discussed from both the operational and conservation points of view.