In this paper we report low temperature neutron diffraction studies on MnSe in order to understand the anomalous behaviour of their magnetic and transport properties. 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.