Different phases in hybrid complexes of Co(II) with cis-4-cyclohexene-1-2-dicarboxylicacid (C6H8-1,2-CO2H=Cy-H2) have been generated depending on the reaction conditions. By microwave-irradiation of the same reaction mixtures at different temperatures we have obtained two new phases Co(C8H8O4) x H2O and [Co2(OH)2.8(Cy-H)1.2]. These phases have been established by XRD, UV-DRS, IR and thermo-gravimetric studies as well as by comparison with the reported phases. In these phases the Cy is found in a cis conformation. It has been seen that microwave synthesis proves to be a rapid and clean method of obtaining new high temperature phases in high purity which are obtained, in an impure state after a long time of hydrothermal synthesis.