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While human hearing can easily identify whistle-like sounds made by dolphins and whales, manually identifying them from the increasingly variety and quantity of underwater acoustic signals (such as other marine life sounds and underwater acoustic communication signals) is undoubtedly laborious. To solve this question, a recognition method based on the frequency modulated feature and harmonic characteristic is analyzed in this paper. A harmonic energy analysis algorithm is proposed and is compared to a harmonic detection method. The experimental results prove that the proposed method could identify the whistle-like sounds with an accuracy over 90% and the traditional one could only reach 50%. The recognition method may be applied to the investigation of marine biological habits and the monitoring of marine ecological environment, and can also potentially be further applied to the detection of bionic communication signal.