Cinnamomum kanehirae Hayata is an endemic tree species known as one of the 5 most precious
softwood species in Taiwan. In recent decades, the demand for a medicinal fungus, Antrodia
cinnamomea T.T. Chang et W.N. Chou has made the wood of C. kanehirae increasingly expensive.
Natural stands of C. kanehirae are decreasing due to illegal logging. For the conservation and
molecular identification of C. kanehirae, molecular markers are required. In this study, Illumina
paired-end sequencing was used to construct C. kanehirae transcriptome data. In total, 58,950
unigenes were gained with an N50 of 1,292 bp after de novo assembly. In total, 20,135 simple
sequence repeats (SSRs) were detected, among which 9,353 SSRs were successfully designed for
primer pairs. In the result, the trinucleotide SSR was the most frequent motif. To date, 301 SSR
primer pairs have been validated in 8 C. kahehirae individuals, and 94 SSR primer pairs could
successfully amplify target DNA. This research generated rich genomic SSR primer information,
which will be valuable with molecular identification, population genetics, conservation, and breeding
studies in C. kanehirae in the future.