Magnetic properties of manganese-doped ZnSe quantum dots with the size of approximately 3.6 nm are investigated. The amount of Mn in the ZnSe quantum dots has been varied from 0.10% to 1.33%. The doping level in the quantum dots is much less than that used in the precursor. The co-ordination of Mn in the ZnSe lattice has been determined by electron paramagnetic resonance (EPR). Two different hyperfine couplings 67.3×10−4 and 60.9×10−4 cm−1 observed in the EPR spectrum imply that Mn atoms occupy two distinct sites; one uncoordinated (near the surface) and other having a cubic symmetric environment (nanocrystal core), respectively. Photoluminescence measurements also confirm the incorporation of Mn in ZnSe quantum dots. From the Curie-Weiss behavior of the susceptibility, the effective Mn-Mn antiferromagnetic exchange constant (J1) has been evaluated. The spin-glass behavior is observed in 1.33% Mn-doped ZnSe quantum dots, at low temperature. Magnetic behavior at a low temperature is discussed.