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<p>Abstract</p> <p>Background</p> <p>Molecular genetic maps provide a means to link heritable traits with underlying genome sequence variation. Several genetic maps have been constructed for <it>Brassica </it>species, yet to date, there has been no simple means to compare this information or to associate mapped traits with the genome sequence of the related model plant, <it>Arabidopsis</it>.</p> <p>Description</p> <p>We have developed a comparative genetic map database for the viewing, comparison and analysis of <it>Brassica </it>and <it>Arabidopsis </it>genetic, physical and trait map information. This web-based tool allows users to view and compare genetic and physical maps, search for traits and markers, and compare genetic linkage groups within and between the amphidiploid and diploid <it>Brassica </it>genomes. The inclusion of <it>Arabidopsis </it>data enables comparison between <it>Brassica </it>maps that share no common markers. Analysis of conserved syntenic blocks between <it>Arabidopsis </it>and collated <it>Brassica </it>genetic maps validates the application of this system. This tool is freely available over the internet on <url>http://bioinformatics.pbcbasc.latrobe.edu.au/cmap</url>.</p> <p>Conclusion</p> <p>This database enables users to interrogate the relationship between <it>Brassica </it>genetic maps and the sequenced genome of <it>A. thaliana</it>, permitting the comparison of genetic linkage groups and mapped traits and the rapid identification of candidate genes.</p>