Abstract: Objective The sporophyte transcriptome of Dicranopteris dichotoma was sequenced by Illumina MiSeq 250 to provide molecular information of its growth, development, metabolism, and the micro evolutionary mechanism. Method The functional annotations, metabolic pathways and microsatellite analysis of some Unigenes were conducted using bioinformatics methods. Result A total of 18 463 296 reads containing 4.62 Gbp of sequence information were generated. A total of 63 169 unigenes were formed by initial sequence splicing, with an average read length of 863 bp and N50 value of 1 587 bp. 26 826 unigenes were annotated using BLASTX searches against the Nr, Nt and SwissProt databases. The unigenes of the transcriptome of D. dichotoma were roughly divided into cellular components, molecule function and biological processes categories of 47 branches by gene ontology, of which related with cellular process cell, binding, metabolism processes and catalytic activities. Further annotated based on COG category, Unigenes could be grouped into 26 functional categories. KEGG pathway analysis showed that Unigenes could be divided into 276 classes based on their metabolic function. Meanwhile, 13 286 SSRs (simple sequence repeats) were mined with repeat motif of 2 to 6 bp by MISA. The trinucleotide repeats were most dominant, accounting for a total of 40.41%. AG/CT (14.45%) and AAG/CTT (12.39%) were the most common repeat motifs. Polymorphic SSR markers were developed from repeat motifs, which could be used for genotyping of different individuals of D. dichotoma. Conclusion A higher quality of transcriptome database was obtained in this study, which could reveal the general characteristics of gene expression in the process of growth and development, and lay the foundation for further gene function mining and the large-scale development of molecular markers of D. dichotoma.