In this paper, an acoustic spectrum signature tracks matching algorithm based on the Manhattan distance and the Euclidean distance of signature vectors, and a multi-frame fusion algorithm are proposed for reliable real time detection and matching of boat generated acoustic signal spectrum signatures. The experiments results have shown that the proposed tracks matching algorithm has the ability to discriminate the tracks from different ships and the ability of matching of the tracks from the same ship; and the spectrum signature detection algorithm has captured the critical features of ship generated acoustic signals. In the process of signal spectrum signature detection, the observation of time and frequency space is structured by dividing input digitalized acoustic signal into multiple frames and each frame is transformed into the frequency domain by FFT. Then, a normalization of signal spectrum vector is carried out to make the detection process more robust. After that, an adaptive median Constant False Alarm Rate (AMCFAR) algorithm is used for the detection and extraction of boat generated spectrum signature, in which an extreme low constant false alarm rate is kept with relative high detection rate. Finally, the frame detections are accumulated to build up the track spectrum signatures.