Complex salts of double-stranded DNA with amphiphilic counterions offer novel opportunities for studies of DNA-lipid interactions. Here the effect of the hydrophobicity of the amphiphilic counterion is in focus. For this purpose, double stranded DNA with didodecyldimethylammonium ions as counterions, DDADNA, is prepared and investigated Ninth respect to microstructure. In particular, in order to monitor the interactions with phospholipids, the phase diagram of the DDADNA/lecithin/water system is determined and compared with the previously determined phase diagram with single alkyl chain counterions, dodecyltrimethylammonium, DTA. In both systems, there is a formation of lamellar and reverse hexagonal phases, where hydrated DNA is sandwiched between bilayers or forms the core of reverse cylindrical micelles, respectively. However, whereas the lecithin lamellar phase can incorporate large amounts of DDADNA, there is in the case of the single chain surfactant, DTADNA, a transition to a bicontinuous cubic phase at higher DTADNA concentrations. The general appearance of the phase diagrams, and in particular the role of counterion hydrophobicity, can be rationalized in a simple geometric model.