Anthropogenic stressors are causing widespread coral mortality, leading to loss of coral cover and decreased structural complexity that threatens reef biodiversity, functioning, and ecosystem services. Reef fishes are intimately linked to coral reef complexity, but we lack a generic understanding of which species are particularly affected by reef flattening and what traits make them susceptible. We used extensive species‐ and trait‐based analyses to build a framework for western Atlantic fish association with both structural complexity and coral cover to better understand the implications of reef degradation. These analyses also highlighted the relative importance of live coral versus the structure it provides to reef fishes, which currently remains unclear. We modeled how 25 biophysical and anthropogenic factors correlated with the densities of 109 fish species across 3292 Floridian reef sites. The importance of a metric of structural complexity and coral cover to the abundance of each species was then isolated. Species with positive associations were categorized as likely future ‘losers' and negative associations as ‘winners'. We predicted that 53% of species will be losers on low‐relief reefs, while only 11% were losers with decreased coral cover. We found morphological, behavioral, and ecological traits, not phylogeny, mediate species' responses to reef degradation and that the loss of structure seemed more critical than the loss of coral cover. Eight traits explained 79.7% of the variation in species' associations with relief and six traits explained 27.8% of associations with coral cover. Smaller, streamlined, habitat and trophic generalists are more likely winners on flattened reefs and large‐bodied predators, among other taxa, are likely losers of reef flattening. Identifying these important traits provides insight into mechanisms that may link fish and complex habitats, which allows us to better predict assemblage‐wide responses to future reef flattening.