This paper provides a comprehensive comparative study of traditional, hybrid, and deep learning (DL) methods for detecting marine species in echograms. Acoustic backscatter data obtained from multi-frequency echosounders is visualized as echograms and typically interpreted by marine biologists via manual or semi-automatic methods, which are time-consuming. Challenges related to automatic echogram interpretation are the variable size and acoustic properties of the biological targets (marine life), along with significant inter-class similarities. Our study explores and compares three types of approaches that cover the entire range of machine learning methods. Based on our experimental results, we conclude that an end-to-end DL-based framework, that can be readily scaled to accommodate new species, is overall preferable to other learning approaches for echogram interpretation, even when only a limited number of annotated training samples is available.