The “Comparative Evolutionary Genomics of Cotton” (CEGC) Web-database resource (http://cottonevolution.info) has been developed as one component of an NSF plant genome center (PI: J. Wendel). The resource contains search and display tools for data types ranging from BAC and genetic map through EST and gene expression. Genetic and physical mapping resources include tools such as CMAP for consensus genetic map data and BACman for BAC and related information. Over the past two years, its transcriptome related data have grown with the addition of new gene expression, EST assembly, functional annotation and marker data. Tools for these data types include those for Cotton EST assemblies that facilitate comparative searches, based on significant BLAST sequence alignments to Arabidopsis thaliana (TAIR9) genes. These also facilitate searches for Cotton EST contigs based on TAIR9 annotations and will soon include TAIR10 data as well. EST assembly views are available along with sequence alignments via the genome browser, GBrowse. SSR data have been added to the resource and the related data tools are being adapted to facilitate these and future diversity data. Bulk data downloads are also available and, where appropriate, submitted to public repositories at NCBI. With respect to gene expression data, our spotted oligo and NimbleGen microarray datasets are available via the resource’s implementation of the Stanford microarray database (SMD). Data displays are in familiar formats since our array of related search tools incorporate community developed tools like CMAP, GBrowse and SMD for data views and additional search functionality.