Asarum spp. are important medicinal plants that have the potential for use in treating various types of fevers. Aristolochic acid is one of the main toxic compounds present in these plants. To improve our understanding of the biosynthetic pathway of aristolochic acid, we sequenced the transcriptome of the root and leaf tissues of Asarum heterotropoides and performed de novo sequence assembly. The data were stitched together to produce 468,357 transcripts with an N50 of 611 bp. The data were annotated with various databases (RefSeq non-redundant proteins [Nr], Swiss-Prot, Kyoto Encyclopaedia of Genes and Genomes [KEGG], Clusters of Orthologous Groups/EuKaryotic Orthologous Groups [COG/KOG], and Gene Ontology [GO]) and were annotated. There were 205,165 transcripts (43.81%) of differentially expressed genes in the roots and leaves, which were shown to be involved in biosynthesis, transport, and catabolism, and 100 genes in defence mechanisms. Three candidate transcripts (TyrDC1, TyrDC2, and TyrDC3) were discovered in these differential genes. TyrDC may be a key enzyme in the biosynthesis pathway of aristolochic acid identified using quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and high-performance liquid chromatography (HPLC). The transcriptome data and analysis presented here lay the foundation for further research into these important medicinal plants.