The European rabbit (Oryctolagus cuniculus) presents a significant conservation and management challenge in Greece. While it has been listed in national biodiversity assessments, its population dynamics on the island of Lemnos demonstrate the characteristics of a highly adaptable and rapidly expanding species, exerting substantial ecological and economic impacts. Addressing this issue requires a spatially explicit understanding of its distribution patterns and habitat preferences, particularly given its extensive population growth over the past three decades. To this end, we conducted 40 field surveys across the island, documenting 1534 presence records of the species. We applied Kernel Density Estimation, Getis‐Ord Gi *, and Anselin Local Moran’s I to identify the spatial distribution patterns and significant hotspots. A spatial lag model was used to quantify hotspot intensity and clustering dynamics, while abiotic, biotic, and anthropogenic factors were analyzed to assess habitat associations. Our results revealed that rabbit hotspots are predominantly concentrated in fertile lowland agroecosystems, with nearly 60% of high‐density areas overlapping conservation zones. Soil and field conditions, grazing‐supporting landscapes, and arable and subsidized agricultural areas emerged as significant predictors of O. cuniculus presence. The observed spatial dependencies indicated that while hotspot intensities and clustering dynamics are influenced by the conditions in neighboring areas, habitat characteristics remain fundamental in shaping their distribution, highlighting the broader landscape‐scale spatial patterns affecting rabbit populations. These findings underscore the necessity of adopting spatially informed management strategies that mitigate agricultural impacts while accounting for interconnected spatial dynamics, providing a foundation for informed decision‐making to manage rabbit populations while balancing conservation and agricultural priorities.