The Northern Mozambique Channel includes the southern part of Tanzania, from Mtwara southwards; the northern Mozambique, the northwest and northeast part of Madagascar, Comoros archipelago, the southern Seychelles, including the Aldabra group, Providence plateau and Farquhar, and the French overseas territories Mayotte and Glorieuse.

Southern part of Tanzania, from Mtwara southwards; northern Mozambique, the northwest and northeast part of Madagascar, Comoros archipelago, the southern Seychelles, including the Aldabra group, Providence plateau and Farquhar, and the French overseas territories Mayotte and Glorieuse.

The oceanography of the Mozambique Channel was unknown until ten years ago, when the existence of highly variable eddies several 100 km across, often in dipoles (an anticyclonic and cyclonic eddy pair) that formed in the region around the Comoros, was discovered. As a result of vorticity imparted into the flow of the SEC as it flows around the tip of northern Madagascar, both cyclonic (clockwise) and anticyclonic (anticlockwise) eddies are generated. At times, a larger gyre is also formed that circulates around the Comoros islands. The Comoros archipelago and banks located in the northern-most section of the Mozambique Channel are likely a causal feature in the formation of eddies and of the Comoros gyre. The Glorioso Front was named for its proximity to Glorieuses Island and may mark the transition from the SEC to the waters of the channel. High levels of connectivity due to the eddies around the Comoros mean the islands may play a key role in maintaining the genetic stock of the channel, and be stepping stones/refuges between the Madagascar and Mozambique coasts.

Because water flows in all directions as a result of the eddies, genetic connectivity throughout the Mozambique Channel is likely very high, particularly in the north, resulting in high retention and recruitment of larvae in pelagic and shallow marine ecosystems, and thereby high resilience of communities and populations.

Over an evolutionary timescale, the geology and oceanography of the Mozambique Channel may have played a key role in driving the evolutionary dynamics of the Western Indian Ocean, maintaining and accumulating species in the northern Mozambique Channel in a biodiversity centre second in absolute numbers to the Coral Triangle region, but with a unique evolutionary history and genetic diversity. Genetic connectivity in the Mozambique Channel shows several overlapping patterns – one of high mixing from north to south and distinct from points farther north (coelacanth), and one showing a barrier at the narrow constriction of the channel, showing southern and northern populations (green turtle). Corals show highest diversity, and indications of high connectivity in the northern Mozambique Channel.

Mayotte and the banks may play a role in inducing and stabilizing the dominant anticyclonic flow of the NE corner of the Mozambique Channel, causing higher temperatures in this zone and a particular marine climate with implications on climate vulnerability of marine systems.

Coral reefs and reef fishes: The Northern Mozambique Channel shelters coral reefs with various geomorphology types varying from a fringing reef formation, patch reefs and submerged banks to a proto (Moheli) and double barrier (Mayotte) and atoll (Aldabra) (Quod et al., 2004) and represents the reef biodiversity centre of the WIO from 161 hard coral species (Aldabra) to 287 species in Norwest Madagascar (Pichon, 2008). Reef fish species also vary from 300 to more than 700 species in Seychelles. 

Sharks and rays: Seychelles represent the richest diversity, with 62 species of sharks and 22 species of rays (Kiszka et al., 2009b). Important aggregation of scalloped hammerhead sharks is observed in Mayotte from July to September (Mayshark, 2009).

Whale shark: whale shark appears seasonally in the area during April/May (Nosy be).

Marine turtles: Moheli, Mayotte, Glorieuses and Aldabra are important nesting sites for green turtle, with up to 5,000 females a year and also up to 500 nesting females of hawksbill a year in Aldabra. Available data tracking for the green shows an important migration between islands and also with East African coasts (Bourjea et al., 2007).

Seagrass: The Northern Mozambique Channel shelters the highest number of species in the WIO, from 7 to 12 species (UNEP, WCMC, 2005).

Coelacanth: The Comorian islands are best known for the largest populations of coelacanth in the world, with largest concentrations on the south-west coast of Ngazidja, and notable numbers at Bimbini, Anjouan. In total, a population size of 500 has been estimated for the Comoros. A few individuals are also accidentally caught in the coast of Tanzania.

Dugong: Only a few individuals are observed in Aldabra, but they are also reported in the Moheli Marine Park and the lagoon of Mayotte (Kiszka et al., 2007). The most important dugong population is in Quirimbas Archipelago in Mozambique.

Seabirds: Up to eight species are recorded in Aldabra, with breeding populations of up to 500,000 individuals in Glorieuses and Farquhar. Important Birds Areas are recorded in north-west Madagascar, Moheli, Seychelles, Glorieuses and Tanzania.

Mangroves: the Northern Mozambique Channel presents several large blocks of mangrove forest, including Mahajamba and Bombetoka bays in Madagascar (> 20,000 ha each).

Marine mammals: High diversity of cetaceans from 10 to 12 species (Seychelles) and important breeding areas for humpback whales during austral winter.

Conservation
•        Development of large seascapes (Tanzania, and Tanzania-Mozambique cross-border site).
•        Development of MPA and fisheries reserves.
•        Development of Local Marine Management Areas.
•        World Heritage Site (Aldabra) and current identification of new one