<p>Synthetic cells emulate fundamental biological behaviors, like growth, metabolism, and mobility, but have lacked genotype-driven selection, which is essential for Darwinian evolution. Here, we introduce libraries of short DNA sequences as genotypes into fuel-dependent peptide-RNA-based coacervate droplets, serving as synthetic cells. By sequencing, we identify sequences that partition in the droplets, revealing strong preferences for guanine-rich and adenine-rich motifs. These sequences affect the synthetic cell phenotype—adenine-rich sequences shorten droplet lifetimes through hybridization. In contrast, guanine-rich sequences kinetically trap droplets via peptide interactions, altering dissolution rates and morphology. This study demonstrates how genotype affects phenotype in synthetic cells, establishing essential design principles for achieving Darwinian evolution in minimal protocellular systems.</p>