Embryonic stem (ES) cells have the ability to undergo indefinite self-renewal in vitro and give rise during development to derivatives of all three primary germ layers (ectoderm, endoderm, and mesoderm), which make them a highly prized reagent in cell and gene therapy. Efficient introduction of various genes of interest into primate ES cells has proven to be difficult. Here, we demonstrated that the self-inactivating HIV-1-based lentiviral vectors constructed by MultiSite gateway technology are efficient tools for the transduction of cynomolgus monkey (Macaca fasicularis) ES (cmES) cells. After antibiotic selection, all of the transduced cells can stably express the reporter gene (humanized Renilla GFP or dTomato) while maintaining their stem cell properties, including continuous expression of stem cell markers, alkaline phosphatase (AKP), OCT-4, SSEA-4, and TRA-1-60, formation of embryoid bodies in vitro and teratomas in vivo containing derivatives of three embryonic germ layers. This approach will provide a useful tool for both gene function studies and in vivo cell tracking of stem cells.