Developing synthetic methods to produce carbon dots (CDs) using natural biomass or other readily available carbon sources are currently being explored. We describe a simple and green synthetic method for preparing fluorescent CDs by water extraction from heat-treated shrimp eggs (SE-CDs). The SE-CDs appeared spherical with an average size of 3.25 ± 1.06 nm. Elemental analysis indicate that the SE-CDs have functional groups such as C-OH, C-O-C, CO, and C-H on the surface which give rise to a series of emissive traps between π-π* states. SE-CDs also showed a broad emission range with excellent quantum yield of 18.5 ± 2.6%. In addition, when compared with commonly used traditional CdSe and CdTe nanocrystals, SE-CDs were bio-tolerable to cell at high doses (200 μgml(-1)) in MTT assay. Thus, SE-CDs are very promising alternatives to semiconductor-based quantum dots for in vitro and in vivo bioimaging applications.