The self-assembly of oppositely charged biomacromolecules has been extensively studied due to its pertinence in the design of functional nanomaterials. Using cryo electronic microscopy (cryo-EM), optical light scattering and fluorescence microscopy, we investigated the structure and phase behavior of PEGylated (PEG: poly(ethylene-glycol)) cationic liposome–DNA nanoparticles (CL–DNA NPs) as a function of DNA length, topology (linear and circular) and ρchg (the molar charge ratio of cationic lipid to anionic DNA). Although all NPs studied showed a lamellar internal nanostructure, NPs formed with short (~ 2 kbps), linear, polydisperse DNA were defect-rich and contained smaller domains. Unexpectedly, we found distinctly different equilibrium structures away from the isoelectric point. At ρchg > 1, in the excess cationic lipid regime, thread-like micelles rich in PEG-lipid were found to coexist with NPs, cationic liposomes and spherical micelles. At high concentrations these PEGylated thread-like micelles formed a well-ordered, patterned morphology with highly uniform inter-micellar spacing. At ρchg < 1, in the excess DNA regime and with no added salt, individual NPs were tethered together via long, linear DNA (48 kbps λ-phage DNA) into a biopolymer-mediated floc. Our results provide insight on what equilibrium nanostructures can form when oppositely charged macromolecules self-assemble in aqueous media. Self-assembled, well-ordered thread-like micelles and tethered nanoparticles may have a broad range of applications in bionanotechnology, including nanoscale lithograpy and the development of lipid-based multi-functional nanoparticle networks.