Brandi Harris is the mother of the two children, 8 year old Rae Meyer and 10 year old Cameron Meyer.
Police say she and Vince Hatch took the children from a house in Iowa Monday.
Harris and hatch live in Hermon.
The father of the children has legal custody.
Authorities in Iowa say hatch has a prior history of assaulting at least one of the children, and an amber alert was issued Monday night.
They are believed to be travelling in a 2004 Toyota RAV four with Maine plate number 6228KJ.