In this study, a method will be developed and applied for estimating biological migration parameters of the biomass of a fishery resource by means of a decision analysis of the spatial behavior of the fishing fleet. The method involves the econometric estimation of a two-stage model. In the first stage an aggregated model of discrete selection is estimated per fishing area by the fleet, together with patch capture function, considering the available biomass in each patch as a non-observed feature by the econometrician in the spatial decision of the fleet. This will allow estimating the monthly biomass availability on different fishing patches. In the second stage, values of biomass obtained from the first stage are used in order to estimate a spatial model of biological migration between patches. This method is proven in the Chilean jack mackerel fishery in Central Southern Chile. The application of the model in this fishery will allow estimating statistically significant migration parameters. Results confirm the existence of a high biomass migration between patches by identifying some migration patterns between the fishing areas studied.