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Background   Dryopteris crassirhizoma  Nakai and  Osmunda japonica  Thunb. are ferns that are popularly used for medicine, as recorded by the Chinese pharmacopoeia, and are distributed in different regions of China. However,  O. japonica  is not record in the Standards of Chinese Herbal Medicines in Hong Kong. Research on identification methods of  D. crassirhizoma  and  O. japonica  is necessary and the phylogenetic position of the two species should be identified. The plastid genome is structurally highly conserved, providing valuable sources of genetic markers for phylogenetic analyses and development of molecule makers for identification.    Methods  The plastid genome DNA was extracted from both fern species and then sequenced on the Illumina Hiseq 4000. Sequences were assembled into contigs by SOAPdenovo2.04, aligned to the reference genome using BLAST, and then manually corrected. Genome annotation was performed by the online DOGMA tool. General characteristics of the plastid genomes of the two species were analyzed and compared with closely related species. Additionally, phylogenetical trees were reconstructed by maximum likelihood methods. The content of dryocrassin of the two species were determined according to the Standards of Chinese Herbal Medicines in Hong Kong.    Results  The genome structures of  D. crassirhizoma  and  O. japonica  have different characteristics including the genome size, the size of each area, gene location, and types. Moreover, the (simple sequence repeats) SSRs of the plastid genomes were more similar to other species in the same genera. Compared with  D. fragrans ,  D. crassirhizoma  shows an inversion (approximately 1.6 kb), and  O. japonica  shows two inversions (1.9 kb and 216 bp). The nucleotide diversity (polymorphism information, Pi) analysis showed that the  psbK  gene and  rpl14 - rpl16  region have the highest Pi value in  Dryopteris , and the  ycf2 -CDS3 and  rpl14 - rpl16  regions show the highest Pi vale in  O. japonica . Phylogenetic analyses showed that the two species were grouped in two separate clades from each other, with both individually located with other members of their genus. The marker content of dryocrassin is not found in  O. japonica .    Conclusions  The study is the first to identify plastid genome features of  D. crassirhizoma  and  O. japonica . The results may provide a theoretical basis for the identification and the application of the two medically important fern species.    Electronic supplementary material  The online version of this article (10.1186/s13020-019-0230-4) contains supplementary material, which is available to authorized users.

Plastid genome and composition analysis of two medical ferns: Dryopteris crassirhizoma Nakai and Osmunda japonica Thunb.