Highly photoluminescent and water dispersible ternary alloyed Mn-doped ZnSeS and core/shell Mn:ZnSeS/ZnS quantum dots (QDs) with pure dopant emission were synthesized through a simple aqueous route using thiolactic acid (2-MPA) as a capping ligand. Transmission electron microscopy and X-ray diffraction show that Mn:ZnSeS nanocrystals are of spherical shape, with a diameter of 2.4 nm and a cubic zinc blende structure. With the overcoating of the ZnS shell, the particle size increases to 3.7 nm, which confirms the epitaxial growth of the shell on Mn:ZnSeS cores. The photoluminescence (PL) quantum yield depends on the Mn loading and reaches 22% for Mn:ZnSeS cores doped with 10% Mn and 41% after the growth of ZnS at the surface of the cores due to the effective elimination of surface-trap states. Mn:ZnSeS QDs exhibit also long PL lifetimes (up to 681 μs) indicating that the emission originates from the spin forbidden Mn 2+ 4 T 1 → 6 A 1 transition. Electron paramagnetic resonance and X-ray photoelectron spectroscopy results suggest that Mn 2+ ions 2 are located at the interface of core/shell Mn:ZnSeS/ZnS QDs. Further, the stability of Mn:ZnSeS/ZnS QDs was also investigated along with their transfer in organic phase using octanethiol.