A control system for an engine having a cylinder is disclosed having an engine valve configured to affect a fluid flow of the cylinder, an actuator configured to move the engine valve, and an in-cylinder sensor configured to generate a signal indicative of a characteristic of fuel entering the cylinder. The control system also has a controller in communication with the actuator and the sensor. The controller is configured to determine the characteristic of the fuel based on the signal and selectively regulate the actuator to adjust a timing of the engine valve based on the characteristic of the fuel.