旗艦種可運用在更廣泛的層面,例如保護珊瑚礁、熱帶雨林等生態系統上,目前塞倫蓋提及黃石公園等保護區已引進此概念進行運作。近年來,一些措舉根據特定地區或物種的保護價值來選擇旗艦種,例如由倫敦動物學會(英語:Zoological Society of London)以及保護國際營運熱點執行的邊緣計畫(EDGE project)。[3]最近,微生物學方面開始以獨特的方式選擇旗艦種,這計劃將涉及微生物地理學,並準備採用特定的物種。此計畫的設定目標是為了建立新的旗艦種選擇機制,這是由於引人注目地旗艦種在分布指標上通常具有顯著的外觀或形態。[26][27]
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