Abstract: The Sasussured involucrata possesses high cold-tolerance capacity, which could be a good experimental model for investigating the cold tolerance mechanism. The S. involucrata Transcriptome Knowledge Base (SITKB) (http://www.shengtingsystemsbiology.com/SaussureaKBase/) is a web-based comprehensive database system implemented via html, Perl and Perl CGI/DBI/DBD, Java and JavaScript programming languages on the web front end and PostgrelSQL Relational Database Management System as the backend for data, annotation and knowledge management. SITKB systems was designated to facilitate cold-tolerance gene mining and knowledge discovery and hosts useful knowledge sets such as datasets of raw sequence data quality control, GC contents of raw and assembled DNA sequences, functional annotation of the assembled contigs, assignment of metabolic pathways to the contigs with coding potential, statistics on the rate of meaningful annotation, and blast comparison against other plant transcriptomes or genomes. The knowledge base system also contains a set of software packages for bioinformatics analysis against its stored datasets. This new knowledge base would provide a resource for data mining and knowledge discovery of the functional genes and pathways responsive to cold perturbation and also enhance the capability for elucidating the cold tolerance mechanism. It also offers genomic data resources and a theoretical foundation to facilitate the molecular breeding of cold tolerant crops.