Phenotype-based screening has been recognized as an important research tool for the discovery of novel therapeutic agents. However, the subsequent identification (ID) of the target of bioactive small molecules has been a major bottleneck in the general application of phenotype-based screening to the drug discovery process. The outcome of conventional target ID methods is significantly influenced by the inherent binding affinity of bioactive small molecules, which can be easily affected by experimental buffer conditions and nonspecific interactions. To overcome these limitations in affinity-based target ID, there has been a community effort to develop new target ID methods. In this review, we focus on the paradigm shift in target ID from noncovalent to covalent bonds and the associated issues in target identification.