Abstract: This study aimed to clarify the potential distribution pattern of seagrass resources in the coastal waters of Hainan Island, identify seagrass diversity hotspots, and assess the spatial association between their suitable habitats and marine ranching areas. Focusing on three dominant tropical seagrass species: Enhalus acoroides, Thalassia hemprichii, and Halophila ovalis, this study integrated field survey data collected from 2021 to 2023, historical species distribution records, and 20 marine environmental parameters. We first conducted Spearman correlation analysis and variance inflation factor (VIF) screening to filter collinear environmental variables. Subsequently, we constructed a maximum entropy (MaxEnt) model combined with a stacking ensemble algorithm. This model was applied to predict the potential suitable habitats of the three seagrass species and quantify the contribution of each environmental variable. We further carried out spatial overlay analysis to identify target seagrass hotspots and calculate their spatial overlap with both existing and planned marine ranches. The MaxEnt model exhibited good predictive performance, with all AUC values higher than 0.8. The high-suitability areas of E. acoroides and T. hemprichii were mainly distributed along the eastern coast of Hainan Island, whereas highly suitable habitats for H. ovalis occurred in scattered shallow-water areas along the northeastern and southwestern coasts. Among the three species, H. ovalis had the largest total suitable habitat area, reaching 5,994.23 km². Dissolved oxygen and annual mean water temperature were the major environmental factors associated with the predicted distributions of E. acoroides and T. hemprichii. Annual mean water temperature and salinity were the key limiting factors that determined the spatial pattern of H. ovalis. Target seagrass hotspots showed obvious spatial overlap with existing and planned marine ranch areas in eastern Hainan. These results can provide scientific support for seagrass conservation, restoration site selection, and the optimized spatial planning of marine ranches.