Crossosoma californicum (Crossosomataceae) is a rare shrub species endemic to the California Channel Islands. Previous studies based on allozymes revealed little genetic variability in this plant species. We have isolated 13 polymorphic microsatellite loci from C. californicum. These loci show intermediate levels of variability, averaging 4.2 alleles per locus and expected heterozygosity of 0.376. Two loci did not fit Hardy–Weinberg expectations with significant deficits of heterozygous genotypes consistent with the presence of null alleles or population subdivision.