Traditional　PCR　instrument　detects　the　temperature　of　reagent　with　contact　measurement,　which　has　several　limitations　such　as　thermal　hysteresis,　reagent　contamination　and　point-measurement.　Thus　an　infra　red　thermometer　is　applied　to　contactlessly　measure　the　temperature　of　reagent.　But　infra　red　thermometer　has　the　defect　of　relatively　high　measurement　noise.　Therefore,　we　propose　a　sequential　dual　Kalman　filter　(Seq-DKF)　algorithm　that　uses　an　iterated　extended　Kalman　filter　(IEKF)　and　a　linear　Kalman　filter　(KF)　to　remove　the　measurement　noise　from　infra　red　thermometer　signals　in　real-time.　In　this　algorithm,　IEKF　and　KF　are　executed　sequentially.　The　former　filter　rapidly　identifies　the　parameter　of　heat　exchange　model　with　a　small　number　of　observations.　The　latter　one　filters　the　temperature　signal　based　on　the　identified　model.　After　specifying　the　heat　exchange　model　and　the　Seq-DKF,　we　apply　the　algorithm　to　the　PCR　instrument　for　testing.　Finally,　the　other　three　filters　are　employed　for　comparison　to　demonstrate　the　effectiveness　of　the　Seq-DKF　algorithm.