The current version of CMD database contains a number of recent updates including: new SSRs, redundancy information, trait/QTL feature, comprehensive collection of cotton genetic maps in the Comparative Map Viewer (CMap), SNP data, enhanced web server tools and new computing infrastructure. Total number of cotton SSRs displayed through CMD has increased from 3,452 SSRs in January of 2006 to 17,448 SSRs (including 312 SSR-containing RFLPs) by July of 2011. Twenty-three cotton genetic maps (including 1 consensus map and 1 reference map) were added to previously available 4 genetic maps in the CMD CMap. The total number of agriculturally important cotton traits displayed through CMD is currently 44, corresponding to 76 trait symbols and 884 mapped QTL positions on 14 cotton genetic maps. The QTL information has been uploaded into the CMap Viewer accessible from the CMD homepage. Traits were annotated with the related information about the trait-associated genetic markers and QTLs. In addition, three major protein databases used in the BLAST and FASTA servers in the Tools section (UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and TAIR Arabidopsis) were updated with the latest versions. Homology searches were performed for 17,448 SSR sequences using all three updated protein databases, and the updated homology results are available on the CMD Downloads page. Finally, the new CMD platform is connected to the Palmetto HPC of Clemson University (6,176 CPU cores, 9,264 GB memory and more than 300 TB storage), which provides sufficient computing resources to support the large size computational jobs submitted by the CMD users.