In this paper we report low temperature neutron diffraction studies on MnSe in order to understand the anomalous behaviour of their magnetic and transport prop-erties. Our study indicates that at low temperatures MnSe has two coexisting crystal structures, high temperature NaCl and hexagonal NiAs. NiAs phase appears below 266 K and is antiferromagnetically ordered at all temperatures while the NaCl phase orders antiferromagnetically at 130 K.