Gracilaria sp. is rich in agar, pigment, carbohydrate and mineral contents. This study aims to determine the content of agar, chlorophyll a, carotenoids and nutrient content (protein, carbohydrate, total lipid, ash, water) in Gracilaria sp. grow in different habitats with high and low salinity. Samples were brought from high salinity (44+0.33) ppt from the reservoir habitat and low salinity (26.98+0.15 ppt) from biofilter's shrimp waste pond habitat. Salinity and water quality parameteres were observed in three different subsites. Agar was extracted by alkali methods. Agar spectra were compared to standard agarose and characterized by FT-IR analysis. Results showed that agar content (25.79 ± 0.28%), chlorophyll a (25.79 ± 0.28 mg/g), carotenoid (5.90 ± 0.07 µmol/g) on low salinity was significantly higher (P<0.05) than high salinity. In high salinity, the agar (6.6+0.34%), chlorophyl a (3.62+0.15, carotenoids (0.71+0.1 µmol/g) contents was lower. The protein level of low salinity (14.4 ± 0.70%) was also significantly higher compared to high salinity (8.15+0.25%), respectively. The total lipid, carbohydrate, water, and ash content were similar. FT-IR analysis spectra show the presence of 3,6-anhydro-L-galactose. These can be useful data concerning optimum salinity in Gracilaria sp. culture.