A vast array of microorganisms, especially bacteria, algae, yeasts, fungi and periphytons have received increasing attention for heavy metal removal and recovery due to their good performance, low cost and large available quantities. They are unlike mono functional ion exchange resins, contains variety of functional sites including carboxyl, imidazole, sulphydryl, amino, phosphate, sulfate, thioether, phenol, carbonyl, amide and hydroxyl moieties. They are cheaper, more effective alternatives for the removal of metallic elements, especially heavy metals from soil and aqueous solution. In this study, the application of microorganisms for removing heavy metal from soil and water, is introduced and described based on mechanisms such as assimilation, adsorption, and biodegradation. The advantages regarding the use of microorganisms to remove pollutants are discussed.