This study was focused on assessing the entire bacterial diversity associated with marine microalgae, Isochrysis galbana by using a metagenomic approach. Here, next generation sequencing technologies have been applied for sequencing of 16S rDNA V3 region.A total of 44 different bacterial genera mostly from the classes Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, Flavobacteriia, Acidimicrobiia, Sphingobacteriia were detected in the study. Overall, the present study enhances the understanding of algal microhabitat in terms of diversity and functional profile of associated bacteria.