Abstract: BMP4 is better known for its critical roles in embryonic development, mesenchymal development, organogenesis of a variety of organs and the initiation and progression of tumor. The predicted functionally important residues and 3D structure will be helpful for understanding the function of BMP4 protein and the relationship with other proteins in the BMP signal pathway. The present study aims to identify some functionally important residues and its interaction with corresponding ligands of BMP4 protein. Here, a total of 100 non-redundant protein sequences of BMP4 from various mammals were retrieved from NCBI database. Of the 100 sequences, only 72 sequences have been selected for multiple sequence alignment and the phylogentic tree was split into 10 evenly distributed partitions, namely P1-P10 in order of evolutionary time cut-off (Fig.1). Based on these results, detailed analyses on the evolutionary conservation information were performed through a variety of bioinformatics tools. Conservative analyses show that the TGF?-propeptide domain contains 22 high conservative residues. However, the TGF-? domain only contains 84 class-specific residues (Fig.3). To further explore the functional binding sites of BMP4 protein, the ligand-binding pockets were predicted using software MetaPocket 2.0. The results show that there exists three binding sites and the ligand-binding sites are surrounded the pockets (Fig.4). This study will provide useful information for identifying key residues from functional regions and predicting unknown functional sites in BMP4 family．