CodonAP is a functional genomics database of Codonopsis pilosula. Users can submit locus IDs to quickly search for co-expression networks, expression profile. Additionally, the basic structural and functional annotations of each gene can be obtained, such as Pfam domains, gene families, KEGG metabolic pathways, GO terms, InterPro annotation, trEMBL annotation, SwissProt annotation and orthologues in 7 species. In addition, several tools are provided, including BLAST, orthologue convertion, sequence extraction and expression value extraction.