The diversity and biological activities of fungi associated with the sponges, were investigated by using a culture-dependent method followed by an analysis of the fungal rDNA-ITS sequences. A total of 79 fungal isolates were isolated from 36 sponge samples at NGHE island in Ha Tien Sea, Kien Giang province of the Mekong Delta of Vietnam, Colonies grew on agar medium during 24 h and mycelia developed in the center of colonies with the growth of brown spores. There were 63/79 isolates had the abilities of antibacterial activity when using agar surface diffusion method to investigate the antibacterial activity with 4 reference bacterial strains including Bacillus cereus; Escherichia coli; Salmonella typhimunum and Staphylococcus aureus; however, there were 14 isolates that made halos (sterile zones) with diameter >2 mm and against 2 – 3 reference bacteria were chosen to be identied based on the nucleotide sequence of the internal transcribed spacer (ITS) rDNA. The sequences from the selected fungal isolates showed high degrees of similarity to those of the GenBank reference strains (99% - 100%), all of them were identified as various species of Aspergillus. Five bioactive compounds were identified in the organic solvent ethyl-acetate. The identification of bioactive chemical compounds are based on the peak area, retention time, molecular weight and molecular formular. GC-MS analysis of Aspergillus fumigatus HN11a strain revealed the existence of the Phthalic acid, di-(1-hexen-5-yl) ester, 3-Nitropropionic acid, 2,6-Dihydroxybenzoic acid 3TMS, and Propanamide, Methylpent-4-enylamine.