For the seed plants, the successful break through the soil after germination is a critical step in their life cycle. Most plants rely on hypocotyl elongation to compete the obstacles on the soil surface. As a result of strong selection, the hypocotyl length varies among plants that live in different environments. In this study, we characterized a mutant that had long hypocotyl (lohy) in Capsella rubella. The candidate gene of lohy is a homolog of long hypocotyl 2 (HY2) in Arabidopsis, which encodes a phytochromobilin synthase and is located in chloroplast. A Crhy2ge null mutant showed the long hypocotyl phenotype similar to lohy mutant and F1 plants resulting from the crossed between lohy and Crhy2ge did not recover the long hypocotyl defects suggesting these two mutants are allelic. In order to identify the regulators of CrHY2, we then used CrHY2-pro to screen a yeast One-Hybrid Library prepared from the Arabidopsis transcription factors (TFs), and identified 35 TFs that interact with CrHY2-pro in yeast. From these, we focused on an interesting TF named REVEILLE2 (RVE2) as REV2 overexpression leads to long hypocotyl. In agreement, we found that CrRVE2 proteins could repress the transcription of CrHY2 both in Capsella rubella protoplast and Nicotiana benthamiana leaves. Unexpected, the negative regulatory correlation between RVE2 and HY2 was found largely conserved in Brassicaceae plants varying in hypocotyl length. Therefore, the genetic circuits consisting of RVE2 and HY2 may represents a highly novel gene-regulatory network that could explain the adaptation of plant species in different environment.