A stock assessment of Ensis macha and Tagelus dombeii for the fishery within the Gulf of Arauco, Chile was conducted from 1996 to 2007. The stock assessment model consisted of: (i) a general model of species-specific population dynamics, ii) models for the observations of annual catches, size composition and catch per unit effort; iii) log-likelihood functions for each segment of information and penalties, and iv) a numerical estimation process. The estimation process allows the simultaneous determination of population parameters such as von Bertalanffy growth parameters, rate of natural mortality at age, fishing mortality rates, selectivity, and recruitment. The results for E. macha show clear signs of overfishing between 1996 and 2007, with a critical condition existing in regards to spawning stock and recruitment; the size and age structure in the landings indicates fishing activities are selecting fish that are smaller than the size at first maturity. In the case of T. dombeii, some signs of over exploitation are also detected but with spawning stock and recruitments healthier than that observed in the case of E. macha. Nevertheless, the size and age structure of the landings shows high dependence on the annual recruitment for the success of the fishery. The parental stocks of both species show clear declining trends, which is strongly affecting recruitments to the fishery. Our results demonstrate that it is critical to decrease the amount of fishing and improve the selectivity of the fishery. If changes towards this direction are not carried out, the sustainability of these fisheries is under threat.