The study was carried out to understand the variability in phytoplankton production (Chlorophyll a) and mesozooplankton diversity from two different shallow coastal regions of south Andaman viz. Port Blair Bay (PBB; the only real urban area among the islands) and Mahatma Gandhi Marine National Park; a Marine Protected Area (MPA) at Wandoor. Seasonal sampling was carried out during the Northeast monsoon (NEM - November 2005), Intermonsoon (IM - April 2006) and Southwest monsoon (SWM - August 2006). Significant (P<0.05) seasonal variation was observed in the environmental variables at both the regions. Higher average chlorophyll a (Chl. a) and mesozooplankton standing stock were observed at PBB compared to MPA, but, the seasonal variation observed was marginal at both the study areas. Chl. a showed a steep increasing gradient from outer to the inner regions of the PBB. The number of zooplankton taxa recorded at both areas was quite similar, but marked differences were noticed in their relative contribution to the total abundance. Enenthough the Copepoda dominated at both areas, the non-copepod taxa differed significantly between the study regions. Dominance of carnivores such as siphonophores and chaetognaths were noticed at PBB, while filter feeders such as appendicularians and decapod larvae were more abundant at MPA. Among the calanoid copepods, thirteen and eleven families were recorded at PBB and MPA, respectively. Twelve species of chaetognaths occurred at both the regions. Larval decapods were predominant at MPA and they belonged to twenty families while at PBB thirteen families and several brachyuran larvae were recorded. In the light of the recent reports on various changes occurring in the coastal waters of the Andaman Islands, it is suspected that the difference in Chl. a as well as the mesozooplankton standing stock and community structure observed between the two study areas may be related to the varying anthropogenic influences.