The Mesopotamian Marshlands or The Garden of Eden, lies in the southern part of Iraq with estimated area of 15000-20000 km2. Historically, the area had pioneering role in the human civilization for over 5000 years. The indigenous people of the area are called “Marsh Arabs” or “Ma’dan” who are the descendants of the Sumerians and Semitic people. The former Iraqi regime (Saddam Hussein) had violently led an aggressive campaign to drain the marshes in 1991. Only %7 of the total area survived this campaign, which caused a mass destruction of the ecosystem and dwellers’ displacement. In 2003, water started to flow back to the area. Yet, the reflooding did not restore the whole former area of the wetlands. Moreover, the new ecosystem influenced the diversity and characteristics of the co-existing species in the area. In 2016, due to the importance of the Mesopotamian Marshlands, the International Union for Conservation of Nature (IUCN) listed three marshes from the area as World Heritage Sites requiring conservation, namely: Hammar, Hwezeh and Central Marshes. The aim of this study is to re-evaluate the ecosystem of those three sites from a biological perspective by examining some challenges that should be dealt with to restore stability to this multi-thousand-year-old system..