The biological accumulation of xanthophyll compounds responsible for differences in yellow colouration of the wheat endosperm is of considerable commercial interest for specific end use products. The xanthophylls biochemical pathway is comprised of around nine major gene groups and associated enzymes involved in the synthesis of various xanthophyll or carotenoid components. The current project seeks to establish a molecular toolbox for exploring the chromosomal location and expression of xanthophyll related genes. Identification of target genes has involved online database searches for gene ontologies and similarity searching with rice or arabidopsis to retrieve wheat sequences. To include the possibility of multiple genes within each group, primer design was based upon the alignment of sequences from related grain species and validated by phylogenetic assessment. This work will assist in the identification of gene candidates for QTL and allelic variation for xanthophyll content and flour colour in Australian wheat germplasm. To date, preliminary results indicate possible involvement of Rab geranylgeranyl transferase I α-subunit genes.