Quantum dots (QDs) originating from two-dimensional (2D) sheets of graphitic carbon nitride (g-C3N4), graphene, hexagonal boron nitride (h-BN), monoatomic buckled crystals (phosphorene), germanene, silicene and transition metal dichalcogenides (TMDCs) are emerging zero-dimensional materials. These QDs possess diverse optical properties, are chemically stable, have surprisingly excellent biocompatibility and are relatively amenable to surface modifications. It is therefore not difficult to see that these QDs have potential in a variety of bioapplications, including biosensing, bioimaging and anticancer and antimicrobial therapy. In this review, we briefly summarize the recent progress of these exciting QD based nanoagents and strategies for phototherapy. In addition, we will discuss about the current limitations, challenges and future prospects of QDs in biomedical applications.