Depression is a common mental disorder, which can be long lasting or recurrent, substantially impairing an individual's ability to function in their daily life. The complex interplay of biological, genetic, and environmental factors is important on the development of the disease. Accumulating evidence shed light on the association of dysbiosis of gut microbiota with depression. Gut microbiota may play an important role in central nervous system function, namely through inflammation, and the hypothalamic–pituitary–adrenal axis, and by affecting neurotransmission. Certain gut microbial strains have been shown to may play either a pathogenic or protective role in the development of depression. Oral intake of probiotics/prebiotic can, therefore, represent a therapeutic approach for depression treatment. However, the relevant scientific work has only just begun, and the available data in this field remain limited. Fortunately, utilization of new sequencing technologies allows the attempt to an expanded research on the association of intestinal bacterial flora and human diseases. In this review, we summarize the role of gut microbiota in depression progression. Probiotics/prebiotic in the treatment of depression was also discussed in other threads.