This study explored the anthropogenic stressors of a coral habitat and predicted the role of a proposed MPA around coral habitat on biodiversity conservation. The study was conducted in the Saint Martin's Island which is located in the south east coastal area of Bangladesh. Data on anthropogenic stressors were collected through intensive stakeholder survey and the role of MPA in biodiversity conservation was explored by utilizing Allometric Trophic Network model. This study identified about 16 anthropogenic stressors for the coral reef ecosystem. Increasing fishing pressure significantly reduced the species biomass while reduced fishing pressure increased the biomass of species. Biomass of the species in the system with no fishing area increased significantly (3–6%) while compared with the species biomass of an area without fishing restriction. Our simulations found that imposing fishing restriction in an exploited system significantly improve the species standing stock. Our model outputs suggest that declaration of MPA is beneficial for conservation of biodiversity. However, for sustainable implementation of conservation initiatives a proper management framework is necessary integrating diverse stakeholders.