Abstract Summary: We present a tool called MRSD (Metabolic Route Search and Design) to search and design routes based on the weighted compound transform diagraph. The search submodule returns routes between a source and product compound within seconds in the network of one or multiple organisms based on data from KEGG. The design submodule designs a route from an appointed compound in an interactive mode. The two complementary functions, Metabolic Route Search and Design, can be broadly used in biosynthesis, bio-pharmaceuticals and the other related fields. Availability: bioinfo.ustc.edu.cn/softwares/MRSD/ Contact: [email protected] Supplementary information: Supplementary data are available at the Bioinformatics online.