Doped quantum dots (d-dots) can serve as fluorescent biosensors and biolabels for biological applications. Our study describes a synthesis of mercaptopropionic acid (MPA)-capped Mn(2+):ZnSe/ZnO d-dots through a facile, cost-efficient hydrothermal route. The as-prepared water-soluble d-dots exhibit strong emission at ca. 580 nm, with a photoluminescence quantum yield (PLQY) as high as 31%, which is the highest value reported to date for such particles prepared via an aqueous route. They also exhibit upconversion emission when excited at 800 nm. With an overall diameter of around 6.7 nm, the d-dots could gain access to the cell nucleus without any surface decoration, demonstrating their promising broad applications as fluorescent labels.