Global change is rapidly reshaping species' habitat suitability ranges, hence leading to significant shifts in the distribution of marine life. Contrasting distributional responses among species can alter the spatial overlap between predators and prey, potentially disrupting trophic interactions and affecting food web dynamics. Here, we evaluate long-term changes in the spatial overlap of habitat suitability ranges for trophically related species, including crustaceans, fish, penguins, and pinnipeds across 12 Large Marine Ecosystems from the Southern Hemisphere, merged into three primary regions: South America, Southern Africa, Australia and New Zealand. To this aim, we first use Boosted Regression Trees (BRTs) to hindcast and project species-specific changes in suitable habitat from 1850 to 2100 under two future climate scenarios: SSP1-2.6 (low climate forcing) and SSP5-8.5 (high climate forcing). We then analyze changes in species habitat suitability and potential predator-prey spatial overlaps. Findings reveal that marine species generally exhibit changes in their suitable habitats, with pronounced shifts towards higher latitudes under the SSP5-8.5 scenario. However, contrasting trends emerge among predators across functional groups and regions of South America, Southern Africa, Australia and New Zealand. These variations highlight the need for species and regional-specific management responses. We also project contrasting spatial mismatches between predators and prey: predators experiencing declines in suitable habitat tend to exhibit greater overlap with their prey in future scenarios, whereas those with expanding suitable habitat show reduced spatial overlap with their prey. This study provides valuable insights that can inform spatial management strategies in response to climate change and illustrate how climate change may weaken species' ability to adapt to climate-driven environmental changes due to trophic disruptions.