<p>Climate change is warming the oceans and altering the way species interact and respond to habitat modification. Explaining species responses to ocean warming based on niche theory has produced contradictory results because strong spatio-temporal structuring of communities reduces the effect of habitat change. So, this review proposes a theoretical framework that distinguishes ocean warming effects on marine communities between neutral processes prevailing at local and metacommunity scales and niche processes prevailing at macroecological scales. The framework disputes the dominant view of exclusive niche-driven effects of ocean warming, building upon two complementary components. First, it shows that marine communities respond to ocean warming according to a spatio-temporal hierarchy. The dominance of spatio-temporal structures in the abundance and diversity of organisms points to the prevalence of neutral processes over the influence of niche. Second, it demonstrates that the stable coexistence of species can be assessed through equalising (neutral) and stabilising (niche) processes. These components can be combined into multivariate hierarchical models, offering a means of applying the proposed framework. New tools are also available that help handle uncertainties inherent to natural systems and process diverse sets of data. This integrative view of niche-neutral processes is intended as a general guideline to help improve the predictability of ocean warming effects on biodiversity.</p>