In this paper, a method is introduced for the classification of call types of red hind grouper, an important fishery resource in the Caribbean that produces sounds associated with reproductive behaviors during yearly spawning aggregations. For the undertaken task, two distinct call types of red hind are analyzed. An ensemble of stacked autoencoders (SAEs) is then designed by randomly selecting the hyperparameters of SAEs in the network. These hyperparameters include a number of hidden layers in each SAE and a number of nodes in each hidden layer. Spectrograms of red hind calls are used to train this randomly generated ensemble of SAEs one at a time. Once all individual SAEs are trained, this ensemble is used as a whole to classify call types of red hind. More specifically, the outputs of individual SAEs are combined with a fusion mechanism to produce a final decision on the call type of the input red hind sound. Experimental results show that the innovative approach produces superior results in comparison with those obtained by non-ensemble methods. The algorithm reliably classified red hind call types with over 90% accuracy and successfully detected some calls missed by human observers.