Phthalates are widely used in polymer materials as a plasticizer. These compounds possess potent toxic variations depending on their chemical structures. However, a growing body of evidence indicates that phthalate compounds are undoubtedly discovered in secondary metabolites of organisms, including plants, animals and microorganisms. This review firstly summarizes biological sources of various phthalates and their bioactivities reported during the past few decades as well as their environmental toxicities and public health risks. It suggests that these organisms are one of important sources of natural phthalates with diverse profiles of bioactivity and toxicity.