Plant carotenoids play an important role in light harvesting, photomorphogenesis, seed setting, and the assembly of the photosystem. More than 700 carotinoid compounds involve in plant biosynthesis, some of plant harmone abscisic acid, Vitamin A and β-carotine show growing evidence of benefit to human. For a better knowledge of carotinoid biosynthesis in Brassica, we compared 22 Arabidopsis thaliana genes and identified 39 full length CDS from Brassica rapa (AA), 110 and 62 unigenes from Brassica napus (AACC), and Brassica olearacea (CC) respectively. Carotinoids genes in these genomes share 78-95% sequence identity with the A. thaliana orthologs and had multiple copies of the different genes. Brassica genes and Arabidopsis genes has similar exon/intron split pattern, since the both are Brassicaceae lineage. However, Insertion, deletion and other size variations will commonly occur between each Brassica genomes. We carried out SNPs and Indels annotation between genes of B. rapa and B. napus (AA genome); B. olearacea and B. napus (CC genome) for understating the functional and non functional genes. Phylogenetic analysis of these genes proves the evolutionary functional conservation in Brassica plants. Also we mined Gene Ontology, Protein domain and motif information of all the genes and uploaded in in-home developed Brassica EST database.