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The most famous animal in this region is the Alaotra Gentle Lemur (Hapalemur griseus alaotrensis), which is only found in the reed and papyrus beds and surrounding marshes of Lake Alaotra. In the past, the lake was also home to huge populations of water birds, the most important ones being the Alaotra Grebe (Tachybaptus rufolavatus) and Madagascar Pochard (Aythya innotata). Nowadays both of them are nearly extinct. Further animals that can typically be seen on and around Lake Alaotra are the Madagascar Tree Boa (Sanzinia madagascariensis) and the Malagasy Civet (Fossa fossana).

Other species have accidentally or intentionally been introduced in Madagascar like the Black and Brown Rat (Rattus rattus and Rattus norvegicus), the frog (Rana tigrina) as well as several fish species, including the Black Bass (Micrtopterus salmoides) and the Fibata (Ophiocephalus sp.).

The natural marsh is dominated by the Papyrus sedge (Cyperus madagascariensis) and the open water is dominated by the Star water-lily (Nymphaea stellata) and the exotic weeds, Salvinia molesta and Eichhornia crassipes.

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