High‐molecular‐mass PC complexes (PC‐HMWCs) constituted by phytochelatins (PCs), cadmium and sulfide are synthesized by several organisms after exposure to cadmium. In this study, PC‐HMWCs were isolated from photoheterotrophic Euglena gracilis and purified to homogeneity, resulting in compounds of molecular mass 50–380 kDa depending on the CdCl₂ and sulfate concentrations in the culture medium. In contrast with plants and some yeasts, PC‐HMWCs from E. gracilis mainly comprise (57–75%) monothiol molecules (Cys, γ‐glutamylcysteine, GSH) and, to a lesser extent (25–43%), PCs. A similar acid‐soluble thiol compound composition was found in whole cell extracts. The –SH/Cd²⁺and S^2–/Cd²⁺ ratios found in purified PC‐HMWCs were 1.5 and 1.8, respectively; the (–SH + S^2–)/Cd²⁺ ratio was 3.2. PC‐HMWCs of molecular mass 60 and 100 kDa were also localized inside Percoll‐purified chloroplasts, in which cadmium and PCs were mainly compartmentalized. Cadmium and sulfur‐rich clusters with similar sulfur/cadmium stoichiometries to those of the purified PC‐HMWCs were detected in the chloroplast and throughout the cell by energy dispersive microanalysis and atomic resolution electron microscopy. The presence of PC‐HMWCs in primitive photosynthetic eukaryotes such as the protist, E. gracilis, suggests that their function as the final cadmium‐storage‐inactivation process is widespread. Their particular intracellular localization suggests that chloroplasts may play a major role in the cadmium‐resistance mechanism in organisms lacking a plant‐like vacuole.