We compared the sequence of a 96.7 Kb-long BAC clone (B 19 N 3) from Brassica oleracea (broccoli) with its corresponding regions in Arabidopsis thaliana. B 19 N 3 contains eight genes and 15 transposable elements (TEs). The first two genes in this clone, Bo 1 and Bo 2, have its corresponding region at the end of chromosome V of Arabidopsis (24 Mb). The third gene, Bo 3, corresponds to an ortholog at the opposite end (2.6 Mb) of the same chromosome. The other five genes, Bo 4 to Bo 8 also have a corresponding region on the same chromosome but at 7.7 Mb . These five genes are colinear with those found in the corresponding region of Arabidopsis, which contains, however, 15 genes. Therefore, a cluster of 10 genes is missing in B. oleracea clone (B 19 N 3). All five genes in common have the same order and orientation in the genomes of both species. Their 36 exons constituting the eight homologous genes have high conservation in size and sequence identity in both species. Among these, there is a major gene involved in aliphatic glucosinolate biosynthesis, Bo GSL-ELONG (Bo 4). Similar to A. thaliana, this gene, has a tandem duplicate, Bo 5. A contig for this region was constructed by primer walking and BAC-end-sequencing, revealing general gene colinearity between both species. During the 20 million years separating A. thaliana from B. oleracea from a common ancestor both genomes have diverged by chromosomal rearrangements and differential TE activity. These events, in addition to changes in chromosome number are responsible for the evolution of the genomes of both species. In spite of these changes, both species conserve general colinearity for their corresponding genes.