We determine the minimal number of separating invariants for the invariant ring of a matrix group G ≤ GLn(Fq) over the finite field Fq. We show that this minimal number can be obtained with invariants of degree at most |G|n(q − 1). In the non-modular case this construction can be improved to give invariants of degree at most n(q − 1).As examples we study separating invariants over the field F 2 for two important representations of the symmetric group.