Despite their rather universal distribution in tropical inter-tidal coastal area mangrove has been identified driven by some physical, chemical and biological factors which might varied one to another site. Muddy waters, sufficient fresh water supply, high tidal inundation were few factors which commonly correlated with an ideal mangrove growth. Ayau Islands, a group of several small island in the Raja Ampat Islands regency West Papua, however, could be an example on how mangrove were closely interconnected to other tropical coastal ecosystem i.e:, seagrasses and coral reef even though grew in a not such “ideal” condition.   A purposive sampling method was applied for this study, two stations was designated in Kanober Island and one station in Dorekar Island. Tree replication sampling plot of 10m x 10m was lied on each station and data were collected following a mangrove monitoring manual.  The result showed at least 4 major species, 3 minor species and 12 association of mangrove component were found in the study site. Bruguiera gymnorriza, Rhizophora mucronata, Rhizophora lamarckii, Ceriops tagal and Sonneratia ovata were the most common species. In general the vegetation in a good condition with a high canopy cover.