[Purpose] There are various treatment modalities for fibromyalgia syndrome (FMS), which is characterized by widespread pain and fatigue. The aim of this study was to investigate the effects of aquatic, aerobic and isometric strength-stretching exercises on the physical and psychological parameters of patients with FMS. [Subjects and Methods] Seventy five female patients with FMS were randomly selected and divided into three groups. Patients (18-50 years) were treated for 3 months using one of three methods: a home-based isometric strength and stretching exercise program (ISSEP), a gym-based aerobic exercise program (AEP), and a pool-based aquatic aerobic exercise program (AAEP). Items evaluated were: the number of tender points, Visual Analog Scale (VAS), Fibromyalgia Impact Questionnaire (FIQ), the Six-Minute Walk Test (6MWT), SF-36 physical and mental health scores, and the Beck Depression Inventory (BDI). [Results] The results revealed that AAEP was the most effective treatment of the three. All of the groups showed significant improvements in all variables between pre-and post-test, except the mean values of VAS and BDI in ISSEP. [Conclusion] The results suggest that aquatic aerobic exercise program is more effective than AEP and ISSEP in the treatment of FMS.