Based on the experimental data of metallothionein-I (MT-I) tertiary structures, interatomic distance constraints of two characteristic structures (CXC, CXXC sequence pattern and metal-Cys chelate tertiary structure) were constructed. Then the distance geometry method was used to work out a number of possible structures, from which those with remarkably lower target function value were selected by a statistical analysis as the predicted tertiary structure models. The predicted structure of blue crab by this method was similar to the experimentally determined structure showed that this method could be used to MT prediction. The tertiary structure of a metallothionein CAP3 from Colletotrichum gloeosporioides was modeled. The predicted structure is similar to those of its homologous MT proteins in metal-Cys combination, and reasonable in its structure energy as well as in its fold motif.