The nanocrystals, so-called quantum dots (QDs), are undisputedly excellent fluorescent markers for imaging and clinical diagnostics. However, their toxicity is always a perturbing issue and remains as the major hindrance for biocompatible imaging and other biomedical applications. Here, we have demonstrated the extraction and application of an extremophilic bacterial polysaccharide, mauran (MR), from a moderately halophilic bacterium called Halomonas maura in the stabilization of ZnS:Mn2+ QDs for the first time. MR has been employed as a natural polymer for bioconjugation to enhance the cellular acceptance and decrease the cytotoxicity of QDs while being used as a fluorescent marker for imaging purposes. Five nanometer-sized QDs were stabilized using an aqueous MR solution under ambient conditions to yield 10–20 nm-sized nanoparticles. Characterization of MR-QD was performed using UV–vis and fluorescent spectroscopy, TEM, SEM, and FTIR. A cytocompatibility assay revealed that the cellular toxicity of QDs was drastically reduced on MR stabilization. In vitro cellular imaging of mouse fibroblast cells and breast adenocarcinoma cells showed that MR-QDs are equally effective as normal QD imaging without imparting any toxicity issues. Thus, it was shown that extremophilic sulfated bacterial polysaccharide, MR, can be successfully used as a novel stabilizing agent for QDs to reduce toxicity and eventually be used as a safe fluorescent agent for in vitro imaging.