The majority of human microbiota resides in the GIT approximately 3.6 x 1013. Identification of gut microbiota composition in obese individuals and defining bacterial community differences between men and females help in the treatment of certain metabolic disorders. The analysis of gut microbiota of men and females was performed with 16s rRNA genes using Illumina MiSeq sequencing. 5 stool samples for each group were collected from obese men and females. In our study, we found that the Alpha diversity was enriched in obese men than obese females this may be due to the hormonal disturbance in the females which make the change in immunity and thereby, change in richness and diversity of gut microbiota composition. Firmicutes / Bacteroidetes ratio was higher in men than females due to the overrepresentation of Firmicutes in men and overrepresentation of Bacteroidetes in case of obese females. Finally, Illumina MiSeq sequencing of 16S rRNA V4 region was allowing cheap and efficient studying of gut microbiota.