This paper describes the synthesis of highly water-soluble and fluorescent ZnSe(S)-alloyed quantum dots (QDs). We used zinc perchlorate hexahydrate, sodium hydrogen selenide as precursors and mercaptopropionic acid as stabilizer to synthesize ZnSe QDs in aqueous solution at 160 °C for 9 h. The as-prepared ZnSe QDs possess a quantum yield (QY) of 8.1% and high trapped emission. After UV irradiation using a 100 W Hg–Xe lamp for 0.5 h, ZnSe(S) QDs having a QY of 19.0% are formed from ZnSe QDs. However, aggregation of ZnSe(S) QDs under longer UV irradiation (> 0.5 h) takes place, leading to instability and irreproducibility. To overcome this, additional thiol compounds (mercaptopropionic acid, mercaptosuccinic acid, 11-mercaptoundecanoic acid, and thioglycolic acid) were separately added to ZnSe QD solutions during UV irradiation. UV irradiation and oxygen accelerate the release of S2− from the thiol compounds, leading to the formation of ZnSe(S) QDs. Among the thiol compounds, mercaptosuccinic acid is the most suitable in terms of stability and photoluminescence intensity. We suggest that the size and functional group of the thiol compounds play an important role in determining the optical properties and stability of ZnSe(S) QDs. The as-prepared ZnSe(S) QDs fluoresce strongly (QY up to 44.0%) at 407 nm with a narrow bandwidth (W1/2 < 25 nm) when excited at 325 nm. [ABSTRACT FROM AUTHOR]