Effects of lattice mismatch on electrical properties of thin n-type ZnSe epilayers grown on GaAs and InP substrates by MOVPE have been investigated. It is shown that the carrier concentration in the epilayer dramatically decreases with decreasing the layer thickness below about 0.5μm. By the DLTS analysis, it has been found that deep levels arising from the lattice mismatch are spatially localized near the heterointerface. It has been found that the defects generated during lattice relaxation seriously affect the electrical properties of the thin epilayers.