As well as the strength check, fatigue life check is also mainly required for designing mooring lines of the floating structures. In general, forces which induce dynamic structural response significantly affect to fatigue design of the mooring lines. So, waves are mainly considered as the governing loading for fatigue design of the mooring lines. In this study, characteristics of the fatigue damage of the mooring lines for submerged floating tunnels (SFT) under irregular waves are investigated. For this study time domain hydrodynamic analysis is used to obtain motion of the tunnel and tension and stresses of the mooring lines under the specific environmental conditions. Also, the Rainflow-counting method, the Palmgren-Miner’s rule, and S-N curves for floating offshore structures presented by DNV recommendation is applied to calculate the fatigue damage due to the fluctuating stresses. Referring to the design plactice of the tendon pipes for TLP (tension-leg platform), which is very similar structural system to SFT, it is assumed that a 100 year return period wave attacks the SFT systems during 48 hours and the fatigue damages due to the environmental loading are calculated. Following the analysis sequence, the effects of the tunnel draft, spacing and initial inclination angle of the mooring lines on the fatigue damage under the specific environmental loadings are investigated.