We developed a suite of tetranucleotide microsatellite loci and applied them to a study of genetic variation across the geographic range of coast redwood [Sequoia sempervirens (D. Don) Endl.]. The objectives of the study were to determine if the microsatellite loci could provide useful information on genetic diversity in this hexaploid species and to investigate earlier reports of divergent lineages within coast redwood. The microsatellite loci were highly variable, yielding a total of 142 alleles. Up to six alleles were detected in each individual consistent with the ploidy of coast redwood and suggesting that parental genomes must have been at least partially homologous. This does not rule out autoployploidy in the evolution of the redwood genome. We treated the microsatellite alleles as presence-absence data and we also estimated full genotypes assuming peak intensities varied with allele dosage. Both types of analyses revealed similar trends. Variation within the 17 watersheds sampled, explained most of the genetic diversity, with less than 4% of the variation attributable to watersheds. Our data showed a weak divergence between more or less continuous populations north of 36.8°N (the Sonoma- Mendocino county border) and disjunct populations south of this latitude. This is further north than indicated from earlier studies of marker systems that would be under selection and may reflect a demographic break. In view of the importance of clonal growth, we suggest that redwood may have difficulty adapting to new climatic conditions or of migrating into displaced habitats with anticipated climate change. Furthermore, the southern lineage of populations is likely to be at greatest risk and is therefore of conservation priority.