A method and apparatus of transmitting control information in a wireless communication system is provided. A sequence corresponding to control information from a sequence set is determined. A reference modulation symbol set corresponding to a mini unit by modulating the sequence is generated. At least one reordered modulation symbol set is generated by reordering and repeating the reference modulation symbol set. The at least one reordered modulation symbol set is reordered in a unit of a subgroup. The reference modulation symbol set and the at least one reordered modulation symbol set are mapped to the plurality of mini units in the resource unit respectively.