The Sequential Ordering Problem (SOP) is an optimization problem used to model many different real applications such as production planning, single vehicle routing problems with pick-up and delivery constraints and transportation problems in flexible manufacturing systems. Ant Colony System (ACS) is a well-known metaheuristic metaphor, and it has been successfully applied to many combinatorial optimization problems, among which the SOP. We present a study on the hybridization of a well-known adaptation of the ACS method to the SOP with a Mixed Integer Linear Programming (MILP) describing the problem, leading therefore to a Matheuristic framework. Different combination of the the ACS algorithm with the MILP are considered, critically analyzed and compared. Computational experiments on the set of benchmarks commonly adopted in the literature show the effectiveness of the novel Matheuristic approaches: the first lower bounds were produced for many instances, together with some new best-known upper bounds. The combination of the bounds also provided an optimality proof for many instances.