The biogas production of seaweed is commonly patterned to conventional digester wherein the anaerobic condition is optimized for terrestrial biomass. The high salt content of seaweed and its different structural component than terrestrial plants may contribute to low conversion efficiency. Hence, freshwater (FW) and thalassic (TH) anaerobic digestion of Ulva species were compared to determine the more suitable condition. Biological hydrolysis pretreatment (BHP) was done to improve methane yield, while NaOH pretreatment (CNP) was employed to minimize the limitation of biological hydrolysis. Higher biogasification efficiencies based on the theoretical methane yield (285.23 mL CH4/g Volatile Solids [VS]) were obtained using biological hydrolysis pretreatment (FW: 27.23%, TH: 63.42%). However, the biogasification time of BHP was twice as long as that of NaOH. Nonetheless, the methane yield of all pretreatments under thalassic (BHP: 180.9 mL CH4/g VS, CNP: 158.19 mL CH4/g VS) was higher than freshwater’s (BHP: 77.66 mL CH4/g VS, CNP: 61.67 mL CH4/g VS), suggesting a superior methane fermentation under thalassic condition.