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Monitoring gatunków i siedlisk polskich obszarów morskich swym zasięgiem obejmuje gatunki i siedliska przyrodnicze związane z obszarami morskimi - nie objęte dotychczas monitoringiem w ramach Państwowego Monitoringu Środowiska, a które są wymienione w rozporządzeniu Ministra Środowiska z dnia 13 kwietnia 2010 r. w sprawie siedlisk przyrodniczych oraz gatunków będących przedmiotem zainteresowania Wspólnoty, a także kryteriów wyboru obszarów kwalifikujących się do uznania lub wyznaczania jako obszary Natura 2000 (Dz. U. z 2014 r., poz. 1713). Prowadzenie monitoringu jest obowiązkiem wynikającym z art. 112 z ustawy z dnia 16 kwietnia 2004 roku o ochronie przyrody, która implementuje zapisy Dyrektywy 92/43/EWG w sprawie ochrony siedlisk naturalnych oraz dzikiej fauny i flory (tzw. Dyrektywy Siedliskowej). 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