Metal pollution has been a great challenge in most industrialized countries as a result of waste generated from industrial activities being introduced into the environment. Unicellular green algae have been considered a potential biological tool for bioremediation of metal pollutants due to its metal sequestration properties. However, methods for further improving unicellular green algae metal sequestration by manipulating metal uptake and tolerance in unicellular green algae have not been studied in detail. In this study, a family metal transport protein named MTP1 - MTP4 from C. reinhardtii were screened by yeast heterologous expression for metal transport activity. MTP1 was able to strongly rescue the Zn and Co sensitivity of the zrc1cot1 strain, MTP3 could weakly mediate Zn and Co growth, but MTP2 and MTP4 appeared to have no Zn or Co tolerance activity. MTP2, MTP3 and MTP4 but not MTP1 could strongly rescue the Mn sensitivity of the pmr1 strain. When MTP4 was over-expressed in C. reinhardtii the strain showed a significant increase in Cd tolerance compared to the wild type, but no significant difference in Mn tolerance and uptake. AtHMA4 a Zn2+ and Cd2+ transporter from the plant Arabidopsis thaliana, which is a member of the Heavy Metal ATPase family, was also expressed in C. reinhardtii. HMA4 full length and C-terminal tail expression strains were screened for Zn and Cd tolerance and uptake. Both sets of strains showed a significant increase in Cd and Zn tolerance and uptake compared to the wild type. Metal tolerance and uptake was compared between the genetically engineered C. reinhardtii strains and unicellular green algal strains that are naturally adapted to metal tolerance which were P. hussi, P. kessleri, and C. luteoviridis. Results showed significant increase in Zn and Cd tolerance and uptake in the natural strains compared to the engineered strains. Therefore in addition to genetically engineered strains, naturally adapted strains could also be used as tools for effective metal bioremediation and pollutant treatment.