One of the biggest problem of human society in 21th century is environmental pollution caused by heavy metals. There are various physical and chemical methods to remove heavy metals, wich are costly and time consuming. So that use of alternative method can affect. Resistance and tolerance ability toward heavy metals have been proved in many microorganisms such as fungi. These organisms use several ways against heavy metals. one of them is chelating. Metallothionein protein is included in these metal chelathors with high affinity with metals. the aim of this study is to investigate the possible role of metallothionein in Trichoderma harzianum tolerance toward zinc. The fungus resistance have been identified in previous studies. After culturing the isolates against zinc and determine the metal uptake in amount of 16/7 mg/g, multiple biochemical and molecular methods such as HPLC, SDS PAGE and PCR, were used to protein identification and concentration determination. Gel electrophoresis result revealed that metallothionein will produce in metal presence and also in its absence, by fungi. Following the HPLC result, it was found that high concentrations of metal leads to protein increase and it nearly becomes double in comparison to before situation. So that the amount of protein in the mycelium treated with metal and control samples were 85/95811 µg/ml and 40/44537 µg/ml respectively. This cause metal homeostasis within cells. Due to the absence of certain sequence of metallothionein in close species to Trichoderma harzianum it was used of conserved areas in different fungi for primer design in molecular identification. After gene amplification by PCR, a band of about 1250 bp was obtained. This sequence encoded a protein fragment with 414 amino acid residues. Finally after sequencing and protein comparing, metallothionein activator was found in tested isolate. The results of this study generally revealed the presence and impact of metallthionein in resistance of tested i