We report here the first successful transfer of T-DNA of Agrobacterium tumefaciens carrying the genes coding for β-glucuronidase (uidA), green fluorescent protein (gfp) and hygromycin phosphotransferase (hpt) to the nuclear genome of the green alga Chlamydomonas reinhardtii. The transformation frequency (which was based on hygromycin resistance phenotype) was 50-fold higher than that of the glass bead transformation. Molecular and genetic analyses performed on transformants revealed the stable nuclear integration and expression of transgenes. The simplicity of Agrobacterium-mediated gene transfer and the high transformation frequency as well as the precision of T-DNA integration will enable further molecular dissection of this important model organism to understand basic plant metabolic processes as well as to exploit the system for biotechnological applications.