Cinnamomum kanehirae, an endemic species in Taiwan, has become rare and endangered because of intensive logging and illegal felling performed to obtain medicinal fungus. To facilitate C. kanehirae conservation, 15 novel microsatellites were developed using a magnetic bead enrichment method. Most of these markers were obtained using cross-species amplification. The number of alleles and observed and expected heterozygosities across loci ranged from 2 to 13, 0.000 to 1.000, and 0.152 to 0.897. These novel markers are useful for population and conservation genetic studies on C. kanehirae and for developing appropriate conservation strategies.