Genetic linkage maps represent the order of known molecular genetic markers along a given chromosome for a given species. This provides an insight into the organisation of a plant genome. In comparative genomics, synteny is the preserved order of genes on chromosomes of related species which results from descent from a common ancestor. Comparative mapping is a valuable technique to identify similarities and differences between species and enables the transfer of information from one map to another and assists in the reconstruction of ancestral genomes. This chapter demonstrates the application of online resources to identify candidate genes underlying a QTL, conduct genome comparisons, identify syntenic regions and view comparative genetic maps in grass and Brassica species.