Modular hybrid structures functionalized to assemble in a controlled manner possess diverse properties necessary for a new generation of complex materials and applications. Here, we functionalized giant unilamellar vesicles and emulsion droplets with biotinylated single-stranded DNA oligonucleotides using streptavidin as an intermediary linker to demonstrate specific and reversible DNA-directed self-assembly into vesicle-droplet hybrid structures. A low molar percentage of PEGylated phospholipids independent of the DNA-based recognition machinery at the supramolecular surface modulated the stability of the system. The reversibility of the aggregation was demonstrated by heating the hybrid structures above the melting temperature of the conjoining double-stranded DNA in the presence of excess biotin. The application of this general assembly control system to diverse multiphase soft materials provides the mechanism to assemble complex modular hybrid systems in a controllable and reversible way, which may provide an advantage where multifunctionality is a target property.