To perform comparative sequence and transcriptome analyses between Brassica rapa and Arabidopsis thaliana, we prepared a B. rapa cDNA microarray using 1,820 (ca. 2 K) cDNA clones selected from 2,166 non-redundant sequences of cDNA library of Chinese cabbage. The gene expression during infection with fungal pathogen Colletotrichum higginsianum and treatments with signaling molecules was analyzed using 2 K B. rapa and 1.2 K Arabidopsis cDNA microarrays. In B. rapa, the results suggested a large correlation coefficient between compatible pathogen C. higginsianum-infection and the treatment with salicylic acid, methyl jasmonate, or ethephon. The expression profiles of 145 counterpart gene sets between the B. rapa and Arabidopsis were distributed in the self-organizing map analysis. The 28% of them indicated similarities in the two species transcriptome. These expressed sequence tag (EST) and microarray data should provide a valuable resource for functional genomics on the crops.