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In this paper, the issue of audio source separation from a single channel is addressed, i.e., the estimation of several source signals from a single observation of their mixture. This challenging problem is tackled with a specific two levels coder-decoder configuration. At the coder, source signals are assumed to be available before the mix is processed. Each source signal is characterized by a set of parameters that provide additional information useful for separation. We propose an original method using a watermarking technique to imperceptibly embed this information about the source signals into the mix signal. At the decoder, the watermark is extracted from the mix signal to enable an end-user who has no access to the original sources to separate these signals from their mixture. Hence, we call this separation process informed source separation (ISS). Thereby, several instruments or voice signals can be segregated from a single piece of music to enable post-mixing processing such as volume control, echo addition, spatialization, or timbre transformation. Good performances are obtained for the separation of up to four source signals, from mixtures of speech or music signals. Promising results open up new perspectives in both under-determined source separation and audio watermarking domains.