The B-cell lymphoma-2 (Bcl-2) family of proteins in the animal kingdom widely regulate the mitochondrial outer membrane permeabilization (MOMP) leading to the formation of a caspase cascade and apoptosis. These were seen in early metazoan evolution which has been identified due to the presence of four short conserved Bcl-2 homology (BH) motifs. The most primitive metazoan, Trichoplax adhaerens also shows the presence of proteins from the Bcl-2 family. Here we report the interaction of two anti-apoptotic proteins from the Bcl-2 family with the BH3 motif of two pro-apoptotic Bcl-2 proteins from Trichoplax adhaerens. We further solved the crystal structure of Trichoplax Bcl2 in complex with BH3 peptide from Bak. A structure based comparison with Human Bcl2:Bax complex reveals the similar BH domains, the hydrophobic binding grove and 8 helices suggesting the conserved nature of Bcl-2. Finally, to further understand the conserved nature of these proteins, we tested the interaction of Bcl-2 proteins from Trichoplax adhaerens with that of Homo sapiens revealing binding which suggests the conserved nature of these proteins.