In this work, we report the synthesis of novel cationic phosphonium gold nanoparticles dispersible in water and dimethyl sulfoxide (DMSO) for their potential use in biomedical applications. All the cationic-functionalising ligands currently reported in the literature are ammonium-based species. Here, the synthesis and characterisation of an alternative system, based on phosphonioalkylthiosulfate zwitterions and phosphonioalkylthioacetate were carried out. We have also demonstrated that our phosphonioalkylthiosulfate zwitterions readily disproportionate into phosphonioalkylthiolates in situ during the synthesis of gold nanoparticles produced by the borohydride reduction of gold(III) salts. The synthesis of the cationic gold nanoparticles using these phosphonium ligands was carried out in water and DMSO. UV-visible spectroscopic and TEM studies have shown that the phosphonioalkylthiolates bind to the surface of gold nanoparticles which are typically around 10 nm in diameter. The resulting cationic-functionalised gold nanoparticles are dispersible in aqueous media and in DMSO, which is the only organic solvent approved by the U.S. Food and Drug Administration (FDA) for drug carrier tests. This indicates their potential future use in biological applications. This work shows the synthesis of a new family of phosphonium-based ligands, which behave as cationic masked thiolate ligands in the functionalisation of gold nanoparticles. These highly stable colloidal cationic phosphonium gold nanoparticles dispersed in water and DMSO can offer a great opportunity for the design of novel biorecognition and drug delivery systems.