Luminescent nanomaterials such as semiconductor nanocrystals (NCs) and quantum dots (QDs) attract much attention to optical detectors, LEDs, photovoltaics, displays, biosensing, and bioimaging. These materials include metal chalcogenide QDs and metal halide perovskite NCs. Since the introduction of cadmium chalcogenide QDs to biolabeling and bioimaging, various metal nanoparticles (NPs), atomically precise metal nanoclusters, carbon QDs, graphene QDs, silicon QDs, and other chalcogenide QDs have been infiltrating the nano-bio interface as imaging and therapeutic agents. Nanobioconjugates prepared from luminescent QDs form a new class of imaging probes for cellular and in vivo imaging with single-molecule, super-resolution, and 3D resolutions. Surface modified and bioconjugated core-only and core-shell QDs of metal chalcogenides (MX; M = Cd/Pb/Hg/Ag, and X = S/Se/Te,), binary metal chalcogenides (MInX; M = Cu/Ag, and X = S/Se/Te), indium compounds (InAs and InP), metal NPs (Ag, Au, and Pt), pure or mixed precision nanoclusters (Ag, Au, Pt), carbon nanomaterials (graphene QDs, graphene nanosheets, carbon NPs, and nanodiamond), silica NPs, silicon QDs, etc. have become prevalent in biosensing, bioimaging, and phototherapy. While heavy metal-based QDs are limited to in vitro bioanalysis or clinical testing due to their potential metal ion-induced toxicity, carbon (nanodiamond and graphene) and silicon QDs, gold and silica nanoparticles, and metal nanoclusters continue their in vivo voyage towards clinical imaging and therapeutic applications. This review summarizes the synthesis, chemical modifications, optical properties, and bioimaging applications of semiconductor QDs with particular references to metal chalcogenide QDs and bimetallic chalcogenide QDs. Also, this review highlights the toxicity and pharmacokinetics of QD bioconjugates.