The present study focused on the bioaccumulation and cytotoxicities of Cd, CdSe quantum dots (QDs) and CdSe/ZnS QDs in Escherichia coli (E. coli, represents prokaryotic system) and Phanerochaete chrysosporium (P. chrysosporium, represents eukaryotic system), respectively. Two types of QDs were characterized by transmission electron microscopy (TEM) and dynamic light scattering. The inductively coupled plasma optical emission spectrometer results showed that the bioaccumulation amounts of CdSe QDs by E. coli and P. chrysosporium were larger than those of CdSe/ZnS QDs due to the smaller particle size and less negative surface charges of CdSe QDs. Confocal microscopy and TEM results showed that there was an interaction between QDs and cells, and QDs have entered into the cells eventually, leading to the change of cell morphology. Plasma membrane fluidities and membrane H-ATPase activities of E. coli and P. chrysosporium decreased gradually with the increasing concentrations of Cd, CdSe and CdSe/ZnS QDs. Results of the cell viabilities and intracellular reactive oxygen species levels indicated that the induced cytotoxicities were decreased as follows: CdSe QDs > CdSe/ZnS QDs > Cd. These findings suggested that the cytotoxicity of QDs was not only attributed to their heavy metal components, but also related to their nanosize effects which could induce particle-specific toxicity. The above results offer valuable information for exploring the cytotoxicity mechanism of QDs in prokaryote and eukaryote.