Fungi are rich sources of biologically active natural compounds, which are used in the manufacturing of wide range of clinically important drugs. Alternaria is a fungal genus that belongs to family Pleosporaceae, and has been known as a promising secondary metabolites producer. However the same fungus showed harmful pathogenicity against different plants causing crops economical losses, and is a common allergen in humans, growing indoors and causing hay fever or hypersensitivity reactions. Alternaria is a multicultural fungal genus widely distributing in soil and organic matter. It includes saprophytic, endophytic and pathogenic species. This review aims to briefly summarize the structurally different metabolites produced by Alternaria fungi, as well as their occurrences, biological activities and functions.