Habitat structure plays an important mediating role in predator-prey interactions. However the effects are strongly dependent on regional predator pools, which can drive predation risk in habitats with very similar structure in opposite directions. In the Mediterranean Sea predation on juvenile sea urchins is commonly known to be regulated by seagrass structure. In this study we test whether the possibility for juvenile Paracentrotus lividus to be predated changes in relation to the fragmentation of the seagrass Posidonia oceanica (four habitat classes: continuous, low-fragmentation, high-fragmentation and rocks), and to the spatial arrangement of such habitat classes at a landscape scale. Sea urchin predation risk was measured in a 20-day field experiment on tethered individuals placed in three square areas 35×35 m2 in size. Variability of both landscape and habitat structural attributes was assessed at the sampling grain 5×5 m2. Predation risk changed among landscapes, as it was lower where more ‘rocks’, and thus less seagrass, were present. The higher risk was found in the ‘continuous’ P. oceanica rather than in the low-fragmentation, high-fragmentation and rock habitats (p-values = 0.0149, 0.00008, and 0.0001, respectively). Therefore, the expectation that juvenile P. lividus survival would have been higher in the ‘continuous’ seagrass habitat, which would have served as shelter from high fish predation pressure, was not met. Predation risk changed across habitats due to different success between attack types: benthic attacks (mostly from whelks) were overall much more effective than those due to fish activity, the former type being associated with the ‘continuous’ seagrass habitat. Fish predation on juvenile sea urchins on rocks and ‘high-fragmentation’ habitat was less likely than benthic predation in the ‘continuous’ seagrass, with the low seagrass patch complexity increasing benthic activity. Future research should be aimed at investigating, derived from the complex indirect interactions among species, how top-down control in marine reserves can modify seagrass habitat effects.