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The study assessed the structure, natural regeneration capacity and Biotic agents of Avicennia marina and Bruguiera gymnorrhiza species in Mida creek, Kilifi County. The study used both cross section and descriptive research design. Avicennia marina species was more dominant with a greater complexity index (A2.7, B0.4), basal area (A588cm2, B484cm2) and mean height (A26m, B10m) compared to Bruguiera gymnorrhiza species with both having an aggregate dispersion pattern. During dry season, Height, and diameter of Avicennia marina had a correlation of 0.56 while Bruguiera gymnorrhiza species had 0.78. During rainy season both had a correlation of 0.67. B. gymnorrhiza species had more straight poles than A. marina species, 75.3% of B. gymnorrhiza trees assessed had straight pole compared to 1.7% of Avicennia marina trees. Both Avicennia marina and Bruguiera gymnorrhiza species had fair regeneration capacity where the number of seedlings was greater than saplings and number of saplings was less than mature trees. Littoraria scabra fed mostly on micro-organisms and algae, Littoraria Glabrata fed mostly on mud surface, Sesarma guttata and Sesarma leptosoma fed on mangrove leaves, Cerithidea decollata fed on deposits and organic matter, Terebralia palustris and Selatium elongatium fed more on algae and leaves, Sesasrmi ortmanni, Metopograpsus oceanicus and Neosarmatium meinerti fed on leaves and young propagules, Barnacles and Oyster bunch on the roots and stems of B. gymnorrhiza species. Biotic agents were insignificant in affecting regeneration capacity of A. marina and B. gymnorrhiza species however combinations with climatic and anthropogenic factors affected Regeneration capacity of the two species.