It is important to find signals of interest (SOIs) when operating sonar systems. A threshold-based method is generally used for SOI detection. However, it induces a high false alarm rate at a low signal-to-noise ratio. On the other side, machine-learning-based detection is performed to obtain more reliable detection results using abundant training data, costing intensive time and labor. We propose a method with favorable detection performance by using a hidden Markov model (HMM) for sequential acoustic data, which requires no separate training data. Since the detection results from HMM are significantly affected by the random initial parameters of HMM, the genetic algorithm (GA) is adopted to reduce the sensitivity of the initial parameters. The tuned initial parameters from GA are used as a start point for the subsequent Baum–Welch algorithm updating the HMM parameters. Furthermore, multiple measurements from arrays are exploited both in determining the proper initial parameters with GA and updating the parameters with the Baum–Welch algorithm. In contrast to the standard random selection of the initial point with single measurement, a stable initial point setting by the GA ensures improved SOI detections with the Baum–Welch algorithm using the multiple measurements, which are demonstrated in passive and active acoustic data. Particularly, the proposed method shows the most confidential detection in finding weak elastic surface waves from target, compared to existing methods such as conventional HMM.