Major Depressive Disorder (MDD) is a common illness worldwide with severe socioeconomic consequences. Several hypotheses have been formulated to explain the physiopathology of depression as well as the mechanism of action of antidepressants but two of them had attracted much attention. The dominant monoaminergic hypothesis of depression links the physiopathology of MDD to a deficiency on cerebral serotonin (5-HT) and/or Norepinephrine (NE) levels; however, the relatively new neurogenic and neurotrophic hypothesis raises the possibility of an impaired neuroplasticity and/or depletion of neurotrophic factors in specific networks resulting on their structural deformity and functional impairment. An enormous body of evidence reported particular neuroadaptations following chronic administration of antidepressant drugs. In this review, we describe major adaptive changes in pre-and post-synaptic 5-HT neurotransmission as well as alterations in gene transcription and neurotrophic factors in response to long-term treatment with conventional antidepressants, new putative ones or novel promising drug candidates, all acting via 5-HT system.