Context <p>Despite widespread invasion of fish species into the Southeastern Mediterranean Sea (SEMS), invaders’ spatial habitat uses and potential habitat niche overlap with endemic species within a reef setting are understudied. Identifying the ecologically relevant scale(s) of rocky reef fishes and predicting their distribution within key habitats can improve our understanding of different species’ seascapes utilization.</p> Objectives <p>We aim to model habitat niches of four invasive and four native fish species, assess niche overlaps and identify key environmental drivers and scales of effect shaping their spatial distributions. Results will inform vulnerability assessments and adaptive ecosystem-based management.</p> Methods <p>We quantified the seascape using a 1&#xa0;m-resolution digital bathymetric model of a SEMS subtidal rocky reef seascape. Habitat suitability was modeled using fish occurrence points and multi-scale spatial predictors, while habitat niche overlap was assessed for all species-pairs.</p> Results <p>Invasive reef fishes exhibit higher niche overlap with native species and broader niche breadths than native-native pairings, consistent with long-term habitat partitioning. This suggests that invasive species can both occupy and extend on the niches of native species. Scale-of-effect patterns were strongly species- and predictor-specific. Topographic predictors describing local seafloor structure generally acted at fine spatial scales, whereas seascape predictors describing habitat amount and configuration showed more variable scale responses.</p> Conclusions <p>Our findings underscore the importance of understanding scale-dependency to optimize the performance of marine Species Distribution Models. This study provides a method and ecological baseline for anticipating distributional shifts of high concern invasive species such as Lionfish (<i>Pterois miles</i>) and Silver-cheeked Toadfish (<i>Lagocephalus sceleratus</i>) across temperate rocky reef systems.</p>