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Animal population abundance is a significant parameter for studies on invasive species that can threaten the ecosystem. Researchers have been developing population estimation methods since the 18th century, in order to evaluate species’ evolution and environmental effects. However, studies on the population density of the invasive species <i>Callinectes sapidus</i> are very limited. The present work, using a simulation model combined with field measurements, examines an innovative methodology for estimating the current population of the invasive species <i>Callinectes sapidus</i> in a shallow Mediterranean coastal lagoon. The methodology presented here builds the first stage of modeling and predicting the evolution of this species’ population in marine environments. The simulation model’s results are validated with an estimation of the total population based on juvenile abundance, and a curvature of the species population estimation based on cage catch is implemented. The simulation experiments presented here show the possibility of a robust prediction for blue crab population estimation.