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This paper presents a genetic algorithm approach with harmonic structure evolution for polyphonic music transcription. Automatic music transcription is a very complex problem that continues waiting for solutions due to the harmonic complexity of musical sounds. More traditional approaches try to extract the information directly from the audio stream, but by taking into account that a polyphonic audio stream is no more than a combination of several musical notes, music transcription can be addressed as a search space problem where the goal is to find the sequence of notes that best models our audio signal. By taking advantage of the genetic algorithms to explore large search spaces we present a new approach to the music transcription problem. In order to reduce the harmonic overfitting several techniques were used including the encoding of the harmonic structure of the internal synthesizer inside the individual's genotype as a way to evolve towards the instrument played on the original audio signal. The results obtained in polyphonic piano transcriptions show the feasibility of the approach.