Abstract. Let F n be a free group of rank n with basis x 1 , x 2 , . . . , x n . We denote by S n the subgroup of the automorphism group of F n consisting of automorphisms which fix each of x 2 , . . . , x n and call it the McCool stabilizer subgroup. Let IS n be a subgroup of S n consisting of automorphisms which induce the identity on the abelianization of F n . In this paper, we determine the group structure of the lower central series of IS n and its graded quotients. Then we show that the Johnson filtration of S n coincides with the lower central series of IS n .