Seven fungal species were isolated from soil samples collected from the University of Sultan Qaboos, Muscat, Sultanate of Oman. The fungal isolates were identified as Aspergillus athecius, A. terreus var. africans, A. flavus, A. terreus, A. foetidus, Fusarium chlamydosporum and F. nygamai. Phytochemical and chromatographic investigation showed variety of secondary metabolites in all of the fugal extracts (extra and intra cellular). The antimicrobial activity of internal and external extracts of the isolated fungal species were screened against Candida albicans, C. glabrata, C. parapsilosis, C. tropicalis, Pseudomonas aeruginosa, Lactobacillus acidophilus, Streptococcus gordonii, S. mutans. The antimicrobial activity of external secondary metabolites was generally better than the internal metabolites. The highest antimicrobial activity (32 mm, 30 mm and 29 mm) was obtained from external secondary metabolites of Aspergillus flavus against Candida tropicals, Candida parapsilosis and Candida albicans, respectively.