A system and method for determining scan chain correspondence including defining a reference scan chain having reference latches and a reference constraint, each of the reference latches having a reference latch logic cone, the reference constraint having a reference constraint logic cone and being associated with one of the reference latches; defining an implementation scan chain having implementation latches and an implementation constraint, each of the implementation latches having an implementation latch logic cone, the implementation constraint having an implementation constraint logic cone and being associated with one of the implementation latches; matching known corresponding scan points between the reference scan chain and the implementation scan chain; and determining scan chain functional correspondence between the reference latches and the implementation latches from the reference latch logic cones with any associated reference constraint logic cone and the implementation latch logic cones with any associated implementation constraint logic cone.