A method for transmitting a reference signal by a base station (BS) in a wireless communication system; and the BS are discussed. The method according to one embodiment includes generating a reference signal sequence; applying an orthogonal sequence to the reference signal sequence; and mapping the reference signal sequence to which the orthogonal sequence is applied to a resource for each antenna port. One antenna port is included any one of first and second antenna port sets, and a configuration of antenna ports contained in each antenna port set is changed according to a number of available resource elements (REs) of a physical resource block (PRB) pair. If the number of available REs is lower than a predetermined threshold value, each of the first and second antenna port sets includes antenna ports corresponding to orthogonal sequences capable of performing despreading using a spreading factor.