The endangered Malagasy sacred ibis (Threskiornis bernieri), is found in the Madagascar mangroves ecoregion as well as certain other western coastal Madagascar habitat and the Seychelles. These Madagascar mangroves shelter highly diverse mollusk and crustacean communities, while capturing sediment that threatens coral reefs and seagrass beds. Although up to nine mangrove tree species have been recorded, most of the Madagascar mangrove stands contain six species in four families: Rhizophoracae (Rhizopora mucronata, Bruguiera gymnorrhiza and Ceriops tagal), Avicenniaceae (Avicennia marina), Sonneratiaceae (Sonneratia alba) and Combretaceae (Lumnitzera racemosa).
Some ot the other notable avian associates of the Madagascar mangroves are: the Madagascar Heron (Ardea humbloti, VU), Madagascar Teal (Anas bernieri, EN), Madagascar plover (Charadrius thoracicus, VU), and Madagascar fish eagle (Haliaeetus vociferoides, CR). The Malagasy kingfisher (Alcedo vintsioides) is also thought to occur in these mangroves. This habitat is important for migratory bird species, such as Common ringed plover (Charadrius hiaticula), Crab plover (Dromas ardeola), Gray plover (Charadrius squatarola), African spoonbill (Platalea alba) and Great White Egret (Egretta alba).
A number of mammalian taxa are found in the ecoregion, chiefly lemurs, tenrecs and bats. The sole terrestrial apex mammalian predator of the ecoregion is the Malagasy civet (Fossa fossana), a Madagascar endemic.
Tenrecs occurring in the ecoregion are: Large-eared tenrec (Geogale aurita), the tiniest extant tenrec; Greater hedgehog tenrec found in the Madagascar mangroves, an insectivorous mammal; Lesser hedgehog tenrec (Echinops telfairi); and Tailless tenrec (Tenrec ecaudatus). Each of these tenrecs is endemic to Madagascar, save for the Tailless tenrec, which is also found on Comoros and a few other islands in the region.
Primates found in the Madagascar consist of several lemur species: the Endangered Verreaux's sifaka (Propithecus verreauxi), endemic to western and southwestern Madagascar; the Vulnerable Black lemur (Eulemur macaco); the Vulnerable Red-fronted lemur (Eulemur rufus); the Vulnerable Sambirano Bamboo Lemur (Hapalemur occidentalis); the Endangered Coquerel's Mouse-lemur (Microcebus coquereli), a Madagascar endemic; the Vulnerable Decken's sifaka (Propithecus deckenii), a western Madagascar endemic; Sambirano Woolly Lemur (Avahi unicolor), a northwestern Madagascar endemic; Pale-forked crown lemur (Phaner pallescens), endemic to western Madagascar; Fat-tailed dwarf lemur (Cheirogaleus medius); and Grey mouse lemur (Microcebus murinus).
Bats occurring here are the Near Threatened Malagasy rousette (Rousettus madagascariensis), a cave rooster capable of navigating the airspace of rather dense intact forest; Vulnerable Madagascan fruit bat (Eidolon dupreanum); Near Threatened Commerson's roundleaf bat (Hipposideros commersonii); Near threatened long-fingered bat (Miniopterus schreibersi); Rufous trident bat (Triaenops rufus); Malagasy giant mastiff bat (Otomops madagascariensis), a Madagascar endemic; Malagasy White-bellied Free-tailed Bat (Mops leucostigma), endemic to Madagascar and the Comoros islands of Anjouan and Moheli; Malagasy slit-faced bat (Nycteris madagascariensis), a narrow endemic to the Irodo River Valley in northern Madagascar; Mauritian tomb bat (Taphozous mauritianus); Trouessart's trident bat (Triaenops furculus), endemic to Madagascar and the outer Seychelles atolls; Manavi Long-fingered Bat (Miniopterus manavi), endemic to Madagascar and Comoros; Grandidier's Free-tailed Bat (Chaerephon leucogaster); Robust yellow bat (Scotophilus robustus); Malagasy mouse-eared bat (Suncus madagascariensis); and Malagasy serotine (Neoromicia matroka). Flying foxes found in the ecoregion are: Madagascan flying fox (Pteropus rufus), an important seed disperser who mates whilst hanging upside down.
Other mammals found in the ecoregion are the Madagascan pygmy shrew (Suncus madagascariensis); The only Rodentia member in the ecoregion is the Dormouse tufted-tailed rat (Eliurus myoxinus).
There are a limited number of reptilian taxa found in the Madagascar mangroves: Snake-eyed skink (Cryptoblepharus boutonii); and aquatic apex predator Nile crocodile (Crocodylus niloticus). Some sea turtles, primarily green turtle (Chelonia mydas, EN) and Hawksbill turtle (Eretmochelys imbricata, CR), nest along the western coast within the Madagascar mangroves. The declining species Dugong (Dugong dugong, VU) is also found in the mangroves.
There is only one amphibian species present in the Madagascar mangroves: Mascarene ridged frog (Ptychadena mascareniensis).
There is particularly high diversity among the fish populations in the Madagascar mangroves,the families of which include: Mugelidae, Serranidae, Carangidae, Gerridae, Hemiramphidae, Plectrorhynchidae and Elopidae. The neighboring coral reefs that are associated with the mangroves have also been noted for extremely high fish diversity.
