Patchy landscapes behave differently from continuous ones. Patch size can influence species behaviour, movement, feeding and predation rates, with flow-on consequences for the diversity of species that inhabit these patches. The ecological processes of patchy seagrass habitats are often substantially different from continuous seagrass meadows. To understand the importance of patchiness on regional species pools, we measured decapod richness and abundance in several seagrass patches with contrasting sizes. Additionally, we evaluated potential drivers of patch-specific species distribution including resource abundance, predator habitat use and the structural complexity of patches. Our results showed a non-random distribution of decapod species: small patches were clear hotspots of diversity and abundance, particularly of large-bodied decapods. Interestingly, these hotspots were characterized by lower nutrient resources, lower canopy height, but also lower predator use. Small fish invertivores such as Coris julis and several species of Symphodus were mostly restricted to large patches where they could potentially find better refuge from their own predators. These resident predators may be critical in clumping predation in large patches with consequences for how biodiversity of their prey is distributed across the seascape. Our results highlight the idea that a habitat mosaic with both large and small seagrass patches would potentially bolster biodiversity because preys and predators may seek refuge in patches of different sizes.