Abstract The annotated Arabidopsis genome sequence was exploited as a tool for carrying out comparative analyses of the Arabidopsis and Capsella rubella genomes. Comparison of a set of random, short C. rubella sequences with the corresponding sequences in Arabidopsis revealed that aligned protein-coding exon sequences differ from aligned intron or intergenic sequences in respect to the degree of sequence identity and the frequency of small insertions/deletions. Molecular-mapped markers and expressed sequence tags derived from Arabidopsis were used for genetic mapping in a population derived from an interspecific cross between Capsella grandiflora and C. rubella. The resulting eight Capsella linkage groups were compared to the sequence maps of the five Arabidopsis chromosomes. Fourteen colinear segments spanning approximately 85% of the Arabidopsis chromosome sequence maps and 92% of the Capsella genetic linkage map were detected. Several fusions and fissions of chromosomal segments as well as large inversions account for the observed arrangement of the 14 colinear blocks in the analyzed genomes. In addition, evidence for small-scale deviations from genome colinearity was found. Colinearity between the Arabidopsis and Capsella genomes is more pronounced than has been previously reported for comparisons between Arabidopsis and different Brassica species.