Water samples were collected from the six stations of Manakudy estuary. During the present investigation of bacterial species presented in the water samples of estuary were Zobellia russellii, Pseudomonas tolaasii, Staphylococcus sp., Helicobacter sp., Escherichia sp., Paracoccus sp., Proteus sp., Maraxella sp, Halmonas sp., Aquasalimonas sp., Neisseria sp. and Marinobacter sp. The dominant bacterial strain Zobellia russellii were finally identified by 16S rRNA sequence analysis The objective of the study of microbial diversity in the estuarine environment is the vital beginning to estimate the major compartment of biodiversity and effective causes of human interferences.