MutL and MutS or their homologues are two crucial proteins of DNA mismatch repair (MMR) system. A new method was described for observation of the interaction between MutS and MutL which is based on the fusion gene/fusion protein technique. Three fusion proteins, MutL-GFP fusion (Trx-His6-GFP-(Ser-Gly)6-MutL), MutL-Strep tagⅡ fusion (Trx-His6-(Ser-Gly)6-Strep tagII-(Ser-Gly)6-MutL) and MutS fusion (Trx-His6-(Ser-Gly)6-MutS), were constructed and expressed in E.coli AD494 (DE3). Interaction assay between MutS and MutL was performed in a 96-well microtiter plate. MutS fusion protein was immobilized on the wells and provided a surface for the interaction between MutS and MutL. Results showed that only after binding of MutS to the mismatched DNA, there was an interaction between MutS and MutL. The binding events could be indicated by GFP signal or the signal generated from alkaline phosphatase and its substrate. In addition, the method based on fusion molecular system also serve as a model for studies on the interactions among other proteins or biomolecules.