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I know the following genera have species native to Africa:

Limnophyton (fluitans)
Vallisneria (spiralis var denserrulata?)
Ottelia ulvifolia
Nymphaea (lotus, etc.)
Ammannia (most of them)
Aponogeton (most of them)
Bacopa (crenata, madagascariensis, monnieri)
Bolbitis heudelotii
Ceratophyllum (submersum and demersum)
Ceratopteris (cornuta, thalictroides)
Crinum
Hydrilla
Hydrotriche hottoniiflora
Lagarosiphon (all)
Lindernia parviflora
Nesaea (all, I believe)
Pistia
Riccia fluitans
 
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