Many genetically modified (GM) crops were used for production of plant-derived edible vaccines and other therapeutic recombinant products. However, GM crops resulted in the ecotoxicological risk of gene transfer because of pollen flow during the past 20 years. The most-commonly used eukaryotic model alga, Chlamydomonas reinhardtii has recently been shown the potential of decreasing this risk. Compared to GM crops, there is no risk of gene transfer because the alga culture can be deserved completely scrutiny under laboratory condition and it do not produce pollen. Recently, we had transformed the chloroplast of Chlamydomonas reinhardtii with two genes, CTB and CV1, which encode cholera toxin B subunit and chimeric antigen CV1 fused CTB with VP1 protein from foot and mouth disease virus (FDMV). The transgenic alga subculture were carried out under different selective conditions. The recombinant antigen in transgenic Chlamydomonas chloroplast was detected by western blotting in a period of subculture time. However, the PCR detection data demonstrated that transgene integrated with chloroplast genome would be lost in a special time when was connected with subculture condition. Although loss of transgenic fragment was an inevitable fate for the green alga, our research data showed the possibility that the presence of transgenic fragment was strictly regulated. Thus, the alga can be used for a safer platform for the production of recombinant product than GM crops.