The seed coat of Brassica napus (canola, oilseed rape) is derived from ovule integuments and contains a layer of palisade cells, which have thick secondary walls. Because cellulosic walls and other indigestible components of the seed coat contribute negatively to the value of oilseeds, efforts are underway to alter seed development. To facilitate these efforts, and to better understand the biology of seed coats, we used a 90,000 element microarray to identify genes whose transcripts were expressed in developing seed coats of B. napus. After dissecting seed coats into three layers, and comparing transcript expression in the middle fraction (which contained the palisade-enriched tissue and bulk of inner integument) to transcript expression in developing hypocotyls, we identified 674 genes whose transcripts were more abundant in the middle fraction of the seed coat. Among these were well-characterized markers of seed coat identity and many genes associated with metabolism of cell wall polysaccharides, flavonoids and various cell wall proteins and transcription factors. Conversely, we identified 1,203 genes whose transcripts were more abundant in the hypocotyl tissue as compared to seed coat, including xylem-specific markers, such as XCP1 and XCP2. We validated 21 of the differentially expressed transcripts using quantitative RT-PCR. The results define a set of transcripts that are highly enriched in the developing seed coat of B. napus.