The epiphytic microbial communities of seagrass (Cymodocea rotundata and Thalassia testudinum) along with sediments and seawater of the seagrass ecosystem of Andaman Sea were assessed for heterotrophic bacterial communities. Young leaves of C. nodosa and T. testudinum sediments and water samples were collected from two different locations at Burmanala and Havelock island. Young leaves were swabbed and transferred into Alkaline peptone water along with 1 gm of sediments and 1 ml of seawater for initial microbial enrichments, followed by culture of microbes in Salt Yeast Extract Agar. Thiosulphate Citrate Bile Salt agar was used for seagrass leaves, sediments and water for culturing of Vibrio like microbes. The observed colonies were morphologically (colour) identified first and then further identification was done by Gram staining and various biochemical tests. Sediment bacterial count was 10-fold higher than seagrass and water column communities. Morphologically 29% of total bacterial colonies identified were of grey and white colour. T. testudinum bacterial epiphytes were 2-fold higher than C. rotundata communities. Gram negative bacterial isolates of Pseudomonas, Vibrios and Aeromonas dominated the bacterial colonies than gram positive bacteria of Bacillus and Micrococcus. Vibrios were only observed on seagrass leaves. Seagrass harboured more gram positive bacterial colonies than gram negative, which were dominated in the sediments of seagrass ecosystem. The bacterial communities of landward site of Burmanala and Havelock were similar whereas 2-fold higher communities were observed at the seaward site of Havelock site on T. testudinum. Seagrass ecosystem bacterial epiphytic communities are diverse in oligotrophic waters.