Chemical genetics is an emerging research field that utilises biologically active small molecules to study biological functions of genes and their products. The direct regulation of the protein function by the biologically active small molecules can alternate the gene mutagenesis studies utilised in conventional genetics. Like conventional genetics, chemical genetics can be divided into two concepts – ‘forward’ and ‘reverse’ chemical genetics. These approaches of chemical genetics have a tremendous impact on both functional genomics and drug development. This review focuses on the two ways in which chemical genetics can be used for therapeutic target mining and their practical application in drug development, particularly, in angiogenesis-related diseases.