DNA-mediated synthesis of nanoparticles with different morphologies has proven to be a powerful method to synthesize and access many exclusive shapes and surface properties. While previous studies employ seeds that contain relatively low-energy facets, such as a simple cubic palladium seed in the synthesis of Pd-Au bimetallic nanoparticles, few studies have investigated whether DNA molecules can still exert their influence when the synthesis uses a seed that contains high-energy facets. Seeds that are enclosed by such high-energy facets or sites are known to act as easy nucleation sites in nanoparticles growth and could potentially suppress the effect of DNA. To answer this question, we herein report DNA-encoded control of morphological evolution of bimetallic Pd@Au core-shell nanoparticles from a concave palladium nanocube seed that contains high indexed facets. Based on detailed spectroscopic and SEM studies of time-dependent growth of the bimetallic nanoparticles, we found that each of 10-mer DNA molecules (T10, G10, C10 and A10) has a unique way of interacting with both the seed’s surface and the precursor. Among them, the most important factor is the binding affinity of the nucleobase to the Pd surface, with the A10 possessing the highest binding affinity and thus capable of stabilizing the seed’s high energy surfaces. Furthermore, for bases with lower binding affinity (T10, G10 and C10) than A10, the growth is completely dictated by the seed’s surface energy initially, but the later growth can still be influenced by the different DNA sequences, resulting in four unique morphologically different Pd@Au bimetallic nanoparticles. The effect of these DNA molecules with medium binding affinity can only be observed when there is more deposition of Au. Based on the above results, a scheme for the DNA controlled growth is proposed. Together these results have provided insights into factors governing DNA-mediated growth of core-shell structures using seeds with high-energy sites, and the insights can readily be applied to other bimetallic systems that adopt seed-mediated synthesis.