Dormancy is an essential developmental program that allows tree adaptation to low temperatures by inducing a bud resting state until the end of the winter. After a prolonged cold period, buds reactivate growth in response to the warm temperatures of the spring. In many Rosaceae species, it is believed that a group of genes encoding MADS-box transcription factors controls dormancy cycle. These genes are similar to SHORT VEGETATIVE PHASE (SVP) from Arabidopsis thaliana and often referred as DORMANCY-ASSOCIATED MADS-BOX (DAM) genes. Although their potential role in tree phenology, the precise function and the mode of action of SVP-like genes during the dormancy cycle are still unknown. By making use of apple tree (Malus x domestica) as a model, we have investigated the function of rosaceous SVP-like genes. We found that most of them show patterns of expression that correlate with particular phases of the dormancy cycle. However, MdSVPa, a MADS-box gene that represses budbreak when it is overexpressed in apple, was ectopically expressed during the whole cycle. We also identified several potential complexes formed by apple MADS-box proteins and interestingly, only complexes containing MdSVPa were able to bind a DNA probe carrying two CArG boxes. In the light of these results, we hypothesized that MdSVPa is an essential component of the transcriptional complexes that regulate dormancy cycle. To unravel the roles of these complexes, we have made use of DNA Affinity Purification followed by massive parallel sequencing (DAP-seq). Our DAP-seq analyses showed that MdSVPa-containing complexes bind to gene targets involved in biological processes that could affect dormancy cycle, such as hormone signaling, cell wall and lignin modifications, sugar transport, cell cycle and flower development, among others. These results allow us to build a tentative model describing distinct roles of MADS-box complexes during the dormancy cycle in apple tree.