In order to understand the morphogenesis difference of Arabidopsis thaliana and Capsella bursa-pastoris and elucidate the difference of auxin distribution, fluorescence quantitative PCR (qPCR) method with the –actin gene as internal reference was used to quantify the expression levels of PIN1, PIN3, PIN7 in the roots, stems, leaves, flowers of the two kinds of plants. The results show that the PIN1 expression in all Arabidopsis thaliana organs is higher than they are in the Capsella organs. The expressions of PIN3 in the stem and flower of Arabidopsis thaliana were 3 and 10 times higher than those in the corresponding organs of Capsella bursa-pastoris. PIN7 expression is also higher in Arabidopsis thaliana than it is in the corresponding organs of Capsella with the expression of PIN7 in the leaf of Aradidopsis thaliana more than 10 times higher than those in the leaf of Capsella bursa-pastoris. PIN3 expression is higher in all tissues of Capsella bursa-pastoris than it is in the Arabidopsis thaliana. The expressions of PIN3 in the stem and flower of Arabidopsis thaliana were 3 and 10 times higher than those in the corresponding organs of Capsella bursa-pastoris. The differential expression of auxin polar transport protein related genes may be the direct reason causing the morphology difference in the two plants.