In this study, chloroplast genomes of 22 species belonging to 22 genera were compared to reveal the general characteristics and structural variation of chloroplast genome of Brassicaceae. The results showed that：(1) the genome size was about 150 kb, and there were 1-5 kb differences among the chloroplast genomes of different plants. The differences in genome size were mainly caused by the difference of LSC length. (2) The gene order of Brassicaceae species was basically the same, no gene rearrangement and inversion event was found. (3) trnY, trnG, ycf15, rps16 genes were lost in some species, petB, petD intron sequences were also lost in individual species. (4) The four boundaries of the genome was relatively conservative, IRaLSC boundary located in the rps19 gene, the IRaSSC boundary located in the ycf1 gene in all species, but the length of rps19 and ycf1 was different on each side of the boundary in different species. The IRbSSC boundary located in the overlap area of the ycf1 and ndhF genes in most species, whereas this boundary changed in Alyssum desertorum and Arabis alpina, lied in ycf1 pseudogene and ndhF genes, respectively. (5) Gene length of 29 proteincoding genes varied among the 22 cp genomes, and the variation was from the differences of intron or the coding sequence. Large fragment deletions were observed of ycf1 gene in the three species. The length of some genes revealed obvious phylogenetic signals. (6) The phylogenetic tree of Brassicaceae which was constructed based on the cp genome data had good resolution, and the evolutionary branched were of high supports. The results of this study showed that the cp genome can provide more evidence for the systematics and phylogeny of plant groups that are with faster evolution and low phylogenetic resolution.