The production of antimicrobial compounds by cyanobacterial strains isolated from oil-polluted and non-polluted areas in Khozestan (Iran) was investigated, comparatively. For this purpose, the antimicrobial activities of supernatant and methanolic extracts from liquid cultures of strains of Phormidium tenue ISC24, Leptolyngbya sp. ISC25, Nostoc sp. ISC26, Phormidium sp. ISC27, Nostoc entophytum ISC32, Chroococcus pallidus ISC39 and Nostoc sp. ISC62 from oil-polluted samples, and strains of Fischerella ambigua ISC4, Calothrix sp. ISC11, Microcheate tenera ISC13, Nostoc sp. ISC17, Chroococcus minutus ISC35, Leptolyngbya sp.ISC38 and Spirulina sp. ISC6 from non-polluted samples, were measured against different gram-negative and gram-positive bacteria and fungal strains using a disc diffusion method. Except for fungal strains of Saccharomyces Cerviciae and Candida albicans, the isolates from non-polluted areas had a higher frequency of antimicrobial activity. In this group, the maximum frequency of effects was observed on B. subtilis with 9 cases, and the minimum frequency was observed on S. cervisiae with only one case. Also in the isolates from non-polluted areas, considerable antibacterial effects were observed on gram-negative bacteria. The strongest antimicrobial activity from the isolates collected from non-polluted areas belonged to the supernatant extracts of Spirulina sp. ISC6 on Bacillus sabtilis, with a 26 millimeter inhibition zone. B. subtilis and S. cervisiae, each with 6 positive effects, showed the maximum frequency of susceptibility to the extracts from the isolates from oil-polluted areas. In this group, the strongest effects were observed from the supernatant extracts of Chroococcus pallidus ISC39 and Phormidium tenues ISC24 on S. cervisiae with inhibition zones of 22 and 20 millimeters diameter, respectively. The antibacterial effects against gram-negative bacteria were not significant in these isolates. In general, a significant distinction in the antimicrobial activity between oil-polluted and non-polluted isolates was observed in the frequency of effects and also in the types of susceptible bacterial or fungal strains.