The true mangrove and mangrove associate species that exist in the sanctuary are Avicennia officinalis, Rhizophora mucronata, Acanthus ilicifolius and Acrostichum aureum—the species of conservation importance.
Stachys officinalis | Salvia officinalis | Avicennia germinans | Avicennia marina | Verbena officinalis | Melissa officinalis | Galega officinalis | Cochlearia officinalis | Avicennia | Veronica officinalis | ''Verbena officinalis'' var. ''officinalis'' | Calendula officinalis | Avicennia officinalis | Sanguisorba officinalis | Magnolia officinalis | Cornus officinalis | Avicennia alba | Anchusa officinalis | Althaea officinalis |
Ashtamudi Estuary has mangroves Avicennia officinalis, Brugiera gymnorrhiza and Sonneratia caseolaris as also 43 species of marshy and mangrove associates including two endangered species Syzygium travancoricum (endangered species according to the Red Data Book of Indian Plants) and Calamus rotang in the Terrestrial system.