For many applications in population genetics, codominant simple sequence repeats (SSRs) may have substantial advantages over dominant anonymous markers such as AFLPs. In high polyploids, however, allele dosage of SSRs cannot easily be determined and alleles are not easily attributable to potentially diploidized loci. Here, we argue that SSRs may nonetheless be better than AFLPs for polyploid taxa if they are analyzed as effectively dominant markers, because they are more reliable and more precise. We describe the transfer of SSRs developed for diploid Mercurialis huetii to the clonal dioecious M. perennis. Primers were tested on a set of 54 male and female plants from natural decaploid populations. Eight of 65 tested loci produced polymorphic fragments. Binary profiles from four different scoring routines were used to define multilocus lineages (MLLs). Allowing for fragment differences within one MLL, all analyses revealed the same 14 MLLs, without conflicting with merigenet, sex or plot assignment. For semiautomatic scoring, a combination of as few as two of the four most polymorphic loci resulted in unambiguous discrimination of clones. Our study demonstrates that microsatellite fingerprinting of polyploid plants is a cost-efficient and reliable alternative to AFLPs, not least because fewer loci are required than for diploids.