MKS in the name Lincoln MKS stands for Mark Sedan. This naming convention is used across most other models in Lincoln's inventory, such as the MKZ, MKT and MKX.
The Lincoln MKS is a replacement for Lincoln's classic Continental sedan. The Lincoln MKZ is another replacement for an old model; its name stands for Mark Zephyr, after the discontinued Lincoln Zephyr.
The Lincoln MKT and MKX model designations refer to form factors, just as the name MKS does. MKX is a crossover SUV, and MKT is a trucklike SUV model. Lincoln's popular Navigator SUV does not share this naming scheme, and remains designated the Lincoln Navigator as of 2015.