Biological experiments and drug screen require the transfer of individual zebrafish embryos into standard multi-well microplates. Manually pipetting embryos into wells is tedious and time consuming. This paper reports a prototype cooperative robotic system capable of transferring zebrafish embryos in parallel and depositing a single embryo per well in a 96-well microplate. A cell holding device was developed to trap multiple embryos in a regular pattern. The cell holding device and a microplate are positioned and aligned along multiple axes by the system. Embryo release strategies were systematically studied and compared. Experiments demonstrated that out of the 1,056 zebrafish embryos used in experiments (i.e., 44 times parallel transfer into 11 96-well plates), 996 wells were successfully filled with one and only one zebrafish embryo, representing a success rate of 94.3%. Further experiments confirmed that the transferred embryos were able to develop into zebrafish with 100% survival rate.