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The aim of this study was to observe the variation in the 5-hydroxytryptamine (5-HT) system between a chronic unpredictable mild stress (CUMS) model and a chronic fatigue syndrome (CFS) model. The total distance, the crossing pieces, and rearing times in the open-field test of the CUMS group and the CFS group were all less than those of the control group to different degrees. The concentrations of tryptophan, 5-HT, and 5-HIAA of the CUMS group were obviously lower than those of the control group. In the CFS model, the concentrations of tryptophan, 5-HT, and 5-HIAA were obviously higher than those of the control group. The expressions of tryptophan hydroxylase-2 (TPH-2) and 5-HT1A receptor in protein level and mRNA level were also different among the three groups. The expressions of TPH-2 and 5-HT1A were higher in the CFS group than in the CUMS group. The expressions of TPH-2 and 5-HT1A receptor were lower in the CUMS group than in the control group. We can find that in different situations of mood disorders, the variation of 5-HT system may also be opposite.