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In recent years, the small pelagic fishery on the Pacific northwest coast of Mexico has significantly increased fishing pressure on thread herring Opisthonema spp. This fishery is regulated using a precautionary approach (acceptable biological catch (ABC) and minimum catch size). However, due to fishing dynamics, fish aggregation habits and increased fishing mortality, periodic biomass assessments are necessary to estimate ABC and assess the resource status. The Catch-MSY approach was used to analyze historical series of thread herring catches off the western Baja California Sur (BCS, 1981–2018) and the Gulf of California (GC, 1972–2018) to estimate exploitable biomass and target reference points in order to obtain catch quotas. According to the results, in GC, the maximum biomass reached in 1972 (at the beginning of fishery) and minimum biomass reached in 2015; the estimated exploitable biomass for 2019 was 42.2×104 t; and the maximum sustainable yield (MSY) was 15.4×104 t. In the western BCS coast, the maximum biomass was reached in 1981 (at the beginning of fishery) and minimum biomass was reached in 2017; the estimated exploitable biomass for 2019 was 3.2×104 t; and the MSY was 1.2×104 t. Both stocks showed a decrease in biomass over the past years and were currently near to point of full exploitation. The results suggest that the use of the Catch-MSY method is suitable to obtain annual biomass estimates, in order to establish an ABC, to know the current state of the resource, and to avoid overcoming the potential recovery of the stocks.