Many fisheries around the world have mixed and multispecies characteristics, and controlling the fishing mortality of the respective species assemblages is a permanent problem. Fisheries are tending to move towards ecosystem-based management strategies and models, and given a latent lack of knowledge regarding inter-specific and ecological relationships, a constant search for pragmatic solutions based on exploitation strategy design is necessary. These strategies should reduce the overexploitation risk for less productive stocks and guarantee the sustainability of this type of fisheries in the long term. In this research we evaluate different Harvest Control Rule (HCR) schemes based on variations in the catch per unit of effort (CPUE) of indicator species in a mixed and multi-specific fishery for small pelagic fish (SPF) in Ecuador. Four Operating Models (OM) are implemented that simulates, under several uncertainty sources, the dynamics of the populations and the fishery controlled by adjustments of the fishing effort of the fleet. These uncertainty sources considered, among others, changes in species' biological traits, productivity shifts and two stock-recruitment relationships. The results show that a control rule based on monitoring indicator species and alternating species when one of them reaches 90 %CPUEMSY, combined with a fishing effort stabilizer, would allow lower overfished risks, as well as a greater stability and long-term sustainability for the fishery. Finally, it is recommended to consider the resilience/productivity capacity of the populations in the design of this HCR type, particularly those less resilient species of the fishery.