In this study, water-dispersible ZnS:Mn nanocrystals were synthesized by capping the surface with conventional and simple structured amino acid ligands: $small{L}$-Glycine and $small{L}$-Alanine. The ZnS:Mn-Gly and ZnS:Mn-Ala nanocrystal powders were characterized by XRD, HR-TEM, EDXS, ICP-AES, and FT-IR spectroscopy. The optical properties were measured by UV-Visible and photoluminescence (PL) spectroscopy. The PL spectra for the ZnS:Mn-Gly and ZnS:Mn-Ala showed broad emission peaks at 599 nm and 607 nm with PL efficiencies of 6.5% and 7.8%, respectively. The measured average particle size from the HR-TEM images were $6.4{pm}0.8$ nm (ZnS:Mn-Gly) and $4.1{pm}0.5$ nm (ZnS:Mn-Ala), which were also supported by Debye-Scherrer calculations. In addition, the degree of aggregation of the nanocrystals in aqueous solutions were measured by a hydrodynamic light scattering method, which showed formation of sub-micrometer size aggregates for both ZnS:Mn-Gly ($273{pm}94$ nm) and ZnS:Mn-Ala ($233{pm}34$ nm) in water due to the intermolecular attraction between the capping amino acids molecules. Finally, the cytotoxic effects of ZnS:Mn-Gly and ZnS:Mn-Ala nanocrsystals over the growth of wild type E. coli were investigated. As a result, no toxicity was shown for the ZnS:Mn-Gly nanocrystal in the colloidal concentration region from 1 ${mu}g/mL$ to 1000 ${mu}g/mL$, while ZnS:Mn-Ala showed significant toxicity at 100 ${mu}g/mL$.