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Coralline algae are important habitat formers found on all rocky shores. While the impact of future ocean acidification on the physiological performance of the species has been well studied, little research has focused on potential changes in structural integrity in response to climate change. A previous study using 2-D Finite Element Analysis (FEA) suggested increased vulnerability to fracture (by wave action or boring) in algae grown under high CO2 conditions. To assess how realistically 2-D simplified models represent structural performance, a series of increasingly biologically accurate 3-D FE models that represent different aspects of coralline algal growth were developed. Simplified geometric 3-D models of the genus Lithothamnion were compared to models created from computed tomography (CT) scan data of the same genus. The biologically accurate model and the simplified geometric model representing individual cells had similar average stresses and stress distributions, emphasising the importance of the cell walls in dissipating the stress throughout the structure. In contrast models without the accurate representation of the cell geometry resulted in larger stress and strain results. Our more complex 3-D model reiterated the potential of climate change to diminish the structural integrity of the organism. This suggests that under future environmental conditions the weakening of the coralline algal skeleton along with increased external pressures (wave and bioerosion) may negatively influence the ability for coralline algae to maintain a habitat able to sustain high levels of biodiversity.