In this study, antifouling and antibacterial properties of polar, semi polar and non-polar bioactive compounds derived from the sea cucumber Holothuria leucospilota were investigated. A series comprising n-hexane, ethyl acetate and methanol extracts from four different organs of sea cucumber (body wall, gonad, digestive tract and respiratory tree) were investigated for their antibacterial and antifouling activity against two species of microalgae, larvae of barnacle Amphibalanus amphitrite and a non-target organism: larvae of Artemia salina. Results showed that the highest antibacterial activity was found in the ethyl acetate extract of body wall against Staphylococcus aureus with minimum inhibitory concentration (MIC) of 0.250 mg/mL. The MIC of ethyl acetate extract of body wall ranged between 0.062 and 0.250 mg/mL against two microalgal strains. All extracts showed moderate to low toxicity against larvae of barnacles. The most pronounced anti-barnacle activity was found in the ethyl acetate extract of body wall with median lethal concentration (LC 50) value of 0.049 mg/mL. Among the twelve extracts, the ethyl acetate extracts of body wall showed the maximum antibacterial and antifouling activities. The bioactive compounds of the ethyl acetate extract of the sea cucumber body wall were determined using gas chromatography coupled with mass spectrometry. Fatty acids and terpenes were the major compounds, which may be responsible for antibacterial and antifouling activity of the ethyl acetate extract of body wall of the sea cucumber H. leucospilota.