Aquatic littoral habitats form an invaluable element for human recreation and economy.During the recent decades they have lost part of their biological diversity, due to human impact. More remote areas, for instance the outer archipelagos, are considered as most valuable in terms of natural and pristine biodiversity. Thus protective measures e.g. founding of nature protection areas and reserves have been directed predominantly there.Our aim was to describe how changing archipelago environmental characteristics in the rocky shores (the most common habitat type), influence the biodiversity of littoral communities in the northern Baltic Sea. Geographic classification of northern Baltic sea- and landscape is formed in a natural way due to the existence of inner, middle, and finally the outer archipelago areas, or zones (in it's most simple form measured by the relation between land and water in the landscape). We found that, littoral environmental characteristics were more uniform within an archipelago zone than between the zones, corroborating the existence of geographic zonation also in the littoral environment. The most important environmental factors shaping littoral communities were arranged in a bipolar way, nutrient levels decrease from the mainland towards the outer archipelago, while marine environmental characteristics increase (salinity, Secchi depth and relative wave exposure). Our results point out an ecotone effect together with a series of gradients, both of which increase the biodiversity in the middle and inner parts of the studied area rather than in the most remote and least human-affected areas. Our conclusion is that if, in a management point of view, high biodiversity is taken as a value in itself, then the inner and middle parts of the archipelago should be preferred in the protection. We argue that measures to protect biodiversity should be aimed there rather than to the outer zones that are traditionally taken as the target for environmental protection work, and where most of nature protection and biosphere areas have been founded. Then, finally, if the natural or pristine biodiversity is valued high, then we should protect the outer archipelago, but that would actually mean protecting areas of lower biodiversity.