Cook the macaroni according to the package directions. Drain well, return to pot, and set aside.
In a medium saucepan, melt the butter over medium heat. Sauté the jalapeño for 1 minute, then add the flour. Cook for 2 minutes more, stirring constantly.
Whisk in the milk and heat to boiling.
Add the mustard and cheeses and stir until smooth.
Pour the cheese sauce over the macaroni and toss. Heat to warm through.