The present study documents the antifouling and toxic properties of seagrasses Syringodium isoetifolium and Cymodocea serrulata. For that, the seagrasses S. isoetifolium and C. serrulata were extracted individually using organic solvents viz. dichloromethane, acetone and methanol. Amongst the extracts, the maximum antimicrofouling and antimacrofouling activities were exhibited by methanol extracts of both the seagrasses. The Minimal Inhibitory Concentration (MIC) of methanolic extracts of seagrasses was ranged from 1.0 to 10µg/ml against test biofilm bacteria and microalgal strains. Similarly, 100% fouling inhibition of limpet Patella vulgata was found at 6.0mg/ml of methanolic extracts of seagrasses. The mussel Perna indica showed 50% of byssal production and attachment inhibition at 21.51±2.03, 17.82±1.07µg/ml and the anticrustaecean activity for 50% mortality of Artemia salina was recorded at 732.14±9.21 and 394.16±5.16µg/ml respectively for methanolic extracts of S. isoetifolium and C. serrulata. The minimal inhibitory and higher lethal concentrations of active methanol extracts shows it׳s less toxic nature. Based on the prolific results, methanol extracts of S. isoetifolium and C. serrulata were subjected to purification using silica gel column and thin layer chromatography. Then the active compounds of the bioassay guided fractions were partially characterized using gas chromatography coupled with mass spectroscopy (GC-MS) and keyed out that fatty acids (C16 to C24) were the major components which responsible for the antifouling properties of the candidate seagrasses.