An encoding apparatus and a decoding apparatus in a transform between a Modified Discrete Cosine Transform (MDCT)-based coder and a different coder are provided. The encoding apparatus may encode additional information to restore an input signal encoded according to the MDCT-based coding scheme, when switching occurs between the MDCT-based coder and the different coder. Accordingly, an unnecessary bitstream may be prevented from being generated, and minimum additional information may be encoded.