The present study conducted at the mangrove ecosystem of Kali estuary. Samples were collected from the three fixed stations for the period of thirteen months from January 2008 to January 2009 at regular monthly interval to identify and quantify the abundance, taxonomy and relative ratio of phytoplankton and zooplankton. In the present study of species diversity of zooplankton groups in the mangrove area, composed of twelve groups comprising fifty two species major share comes from the copepods which comprises about seventeen species.  Protozoa taxa comprised by five species, coelenterata and cladocera by two species each, ctenophore comprised by single species whereas the larval forms comprised by fourteen species. Keywords: Zooplankton, Diversity, Abundance, Estuary, Mangrove, Karwar.