Over the past two decades, there has been intense interest in designing and implementing selective (bioorthogonal) reactions for biomolecule tracking. Here we review the most widely used bioorthogonal chemistries in live cells and animals, drawing particular attention to the unique functional groups underlying these transformations. We also describe recent efforts to tune functional group reactivities and stabilities to access even more rapid and selective chemistries. Last, we highlight ongoing challenges in identifying new bioorthogonal reagents and combinations of reactions that can be used concurrently to tag multiple biomolecules.