This study investigates the application of artificial fish swarm algorithm (AFSA) in the power allocation for multiple-input and multiple-output orthogonal frequency-division multiplexing (MIMO-OFDM) relay underwater acoustic (UWA) communication systems. First, by using the singular value decomposition technique, the two-hop transmission links are converted into the virtual direct links in an single-input and single-output OFDM (SISO-OFDM) system. Then, a power allocation optimisation problem, together with the assignment of subcarriers and relay nodes, are formulated for the virtual SISO-OFDM system. Finally, the problem-solving algorithms are proposed in two parts. Computer simulation results show that the proposed AFSA scheme improves in both power consumptions and diversity gains compared with two existing schemes for UWA communication systems.