Global coral reef habitats are in drastic decline in response to rising Ocean temperatures and prolonged heat waves which, alongside other stressors, are causing extensive coral bleaching events. Especially in the Caribbean, continuous coral mortality from bleaching episodes combined with the demise of branching Acropora coral spp. and the loss of the keystone herbivore Diadema antillarum, in the 1980’s induced significant degradation of the physical reef structure. This region-wide "flattening" of the reef matrix equated to a loss of critical habitat for many species. Especially reef fish displaying high site fidelity such as territorial damselfishes are likely affected by long-term habitat alterations. These keystone algae-farmers depend on complex coral structures such as Acropora spp. and have been shown to undergo habitat shifts towards coral species potentially more susceptible to their gardening activities. They are known to exert positive and negative effects on coral and algal survival and likely play a significant role in future Caribbean reef resilience. This study evaluated the distribution of the territorial damselfishes Stegastes planifrons and Stegastes diencaeus in relation to environmental variables and structural reef complexity in the Cayman Islands. Differential structural metrics of micro-habitats were quantified to evaluate whether benthic complexity is of equal importance as a factor of habitat-quality. While both species are highly territorial, S. planifrons is regarded as a greater habitat specialist due to its strong preference for branching corals. Abundances were recorded and compared between northern (semi-exposed) and western (sheltered) shallow and deep reef terraces of Grand Cayman. High-resolution photogrammetric technology was utilized to rapidly capture the physical formation of reef sections and singular territories. Structural complexity metrics (fractal dimension (FD); two-dimensional surface area (m2)) were then extracted from the re-constructed 3D-models. On the shallow reef terraces, correlations of abundances with transect complexity were explored. Finally, territories within shallow western transects were compared regarding home-range sizes and mean complexity values. Environmental variables such as exposure, depth and protection status significantly affected abundances of S. planifrons and S. diencaeus on the reef terrace scale, causing similar distribution patterns. Large abundance variations between sites similar in exposure and depth indicated that other factors are also at play in shaping observed distributions. Both species were positively correlated with transect complexity, yet this trend was less significant for S. diencaeus. On the microhabitat-scale, S. planifrons territories exhibited significantly higher mean complexity than those of S. diencaeus. Only S. planifrons home-range sizes were positively correlated to complexity, indicating that defence efforts increase with habitat quality. These results demonstrated that the FD score can provide a useful metric to quantify habitat quality for S. planifrons. For S. diencaeus, different habitat metrics may be of greater importance for microhabitat distribution and defence. Based on the results from this study and similar trends observed elsewhere, this species may be able to adapt better to the less heterogenic communities of future coral reefs, while stronger habitat-specialists such as S. planifrons could display abundance reductions. Understanding how these species are associated to the reef-structure on different resolution-scales is essential in determining their significance in terms of future reef resilience. The modern mapping methodologies used in this study, in interrelation with fish population ecology, have become important tools for the continuous monitoring and management of these threatened ecosystems and will likely become common practice in marine landscape ecology.