Abstract We evaluate the effective secrecy throughput (EST) of multiple-input-multiple-output relay-assisted free-space optical communication, where legitimate nodes (Alice, Relays, and Bob) communicate in the presence of multiple Eavesdroppers (Eves) under two different weather conditions, namely clear weather with weak turbulence and light fog with strong turbulence. We consider multiple paths between Alice and Bob, each composed of multiple relays, which are capable of operating under: (i) adaptive scheme with selective relaying, where Alice possesses instantaneous channel state information (CSI) of the legitimate channels and selects the optimum path to Bob; (ii) fixed-rate scheme with all-active relaying, where instantaneous CSI is not available and the information is transmitted through all paths. Our results indicate that both schemes benefit from multiple hops, while the use of multiple paths benefits only the adaptive scheme. Furthermore, we also show that the effects of the weather conditions become more relevant with the increase of the distance between Alice and Bob, and that such deterioration in performance can be decreased through the use of relaying nodes.