The Central Baltic Programme covers the whole programme area (Estonia, Finland including Åland Islands, Latvia and Sweden). Projects applying for funding from the Central Baltic Programme must have partners from at least two of these countries. Bilateral Finnish-Estonian projects as well as projects focusing on sea islands and archipelago issues, however, have to apply for funding from the Southern Finland – Estonia or the Archipelago and Islands Sub-programme.

The programme area of the Southern Finland – Estonia Sub-programme covers the participating regions in Southern Finland (except Åland Islands) and Estonia. Projects applying for funding from the sub-programme have to have partners from both Southern Finland and Estonia. Projects focusing on sea islands and archipelago issues, however, have to apply for funding from the Archipelago and Islands Sub-programme.

The Archipelago and Islands Sub-programme covers municipalities with archipelago parts, archipelago municipalities and islands in Estonia, Finland including Åland Islands and Sweden. Projects applying for funding from the sub-programme have to have partners from the Central Baltic Programme area from the countries participating in this sub-programme and at least one partner from the Archipelago and Islands Sub-programme area. Further, project activities should always benefit the island and archipelago parts of the sub-programme area.