Light, auxin and brassinosteroid play important roles in plant growth and development. Genetic analysis has demonstrated complex interactions between their signaling pathways, but the gene regulatory mechanisms connecting these pathways are poorly understood. CYP72B1 and AUR3 are two important genes responsive to light, auxin and brassinosteroid at transcription level. To understand the regulation mechanism of the two genes, a new tool called OCMMat was developed for identifying cis-elements, OCMMat combines both the over-representation property of regulatory elements in co-expressed genes and the conservation property in orthologous genes, for the latter, it was estimated by an enrichment score of regulatory element in orthologous promoter sequences. Using this tool, 3 regulatory motifs shared by genes CYP72B1 and AUR3 were reported, motif GAGACA which is the same as a known cis-element AuxRE, motif AAGAAAAA containing the sequence of GT element and the third ATCATG which is a new one named EDIB element. The space and the order of AAGAAAAA and EDIB show the same pattern in promoters of both the co-expressed genes and the orthologs of CYP72B1. Based on the sequence analysis and the literature knowledge to date, a model was proposed for describing the transcriptional regulatory mechanism of CYP72B1 and AUR3 in response to light, auxin and brassinosteroid. The model presents how the signaling pathways of light, auxin and brassinosteroid are interplaying at gene transcription level. In response to light, the transcription factors GT factor and an unknown protein repress the expression of CYP72B1 and AUR3, the hormone pathways are not interfered and thus work in their own way. While in the absence of light stimulation, CYP72B1 and AUR3 are expressed and the products, in turn, inhibit both the auxin pathway and the brassinosteroid pathways. On the other side, at high hormone level, gene expression is up-regulated through ARF binding, the gene products inhibit the hormone pathways in a feedback manner, and meanwhile, rescues the light signal through the photoreceptor phyB.