Baker cypress (Hesperocyparis bakeri [Jeps.] Bartel) is one of 10 species of cypress found in western North America. It is restricted to a small number of highly disjunct, isolated populations, making it particularly vulnerable to the influences of genetic drift, inbreeding, and reduced gene flow. Baker cypress is fire adapted and the serotinous cones require heat to open and release seeds. Altered fire regimes have negatively impacted the health and vigor of some populations and lower levels of genetic diversity could make this species more susceptible to the impacts of predicted future climate change. Previously, no information on genetic diversity and population structure of Baker cypress was available. We used 12 polymorphic allozyme loci to assess genetic diversity and population structure for eight of the 11 known populations of Baker cypress. Overall mean observed heterozygosity (H_o) was 0.178 and expected heterozygosity (H_e) was 0.204, values higher than for other cypress species and other fire adapted conifers. Although genetic diversity was relatively high, many populations had a deficiency of heterozygotes (fixation index > 0), most likely due to inbreeding and possibly a Wahlund effect. Population differentiation among seven of the eight populations (northernmost population excluded) was 9%, considerably lower than for other conifers with disjunct populations. Our results indicate that the current population structure of the species is likely a fairly recent reduction from a formerly widespread distribution with differentiation among populations resulting from genetic drift. Implications of genetic diversity and population structure for potential restoration work are discussed.