The fish assemblages of two artificial reef systems of the south coast of Algarve (Portugal) are presented, and a comparative study is made of their species richness variation according to their location off the Ria Formosa lagoon. Each system consists of a protection reef and an exploitation reef. Gillnets, traps, longline and visual census were used as sampling techniques. Both reefs showed similar species richness, in each case higher than that of Ria Formosa. No significant differences of species richness were found between the reef systems (p = 0.1). However, the exploitation reefs showed a significant difference of species richness, that was more evident when accumulated species richness was used to compare them (p = 0.01).