A method and an apparatus for transmitting a reference signal in a wireless communication system are provided. A first base station maps a first reference signal to a resource region and transmits the first reference signal to a user equipment. A second base station maps a second reference signal to said resource region and transmits the second reference signal to said user equipment. The resource elements, to which the first reference signal and the second reference signal are mapped in the resource region, are determined in accordance with the index on a Latin square matrix occupied by two different elements, respectively, from among N elements constituting the Latin square matrix with a size of N×N.