The capacity to detect and predict the responses fo marine populations ans communities to the establishment of MPA depends on the ability to distinguish between the influences of management and natural variability due to the effects of factors other tha, protection. Thus, it is important to understand and uantify the magnitude and range of this natural variability at each scale of observation. here we review the scale of responses of target populations and communoties to protectection within Mediterranean MPAs, agianst compare those with documented cases from other temperate ans tropical marine ecosystems. Additionally, we approach the problem of the relative importance of habiata structure, considered as a set of biological and physical elements of the seascape hierarchically arranged in space at multiple scales, to drive natural variability. We conclude that much more effort has to be made to characterize heterogeneity in relation to Mediterranean MPAs, and to quantify and explain relationships between target species ans their habitats as sources of such variability. These studies should be based on sound sampling designs, which (1) generate long-term data sets, and would ideally (2) be based in a Mediterranean-wied comparaison of a number of protected ans unprotected localities, (3) ne designed from a multi-scaled perspective, and (4) control for factors other tha protection, on order to avoid their confoundinf effects. The need for appropriate spatial and temporal replication, nested designs and power analysis is advocated.