In time, it is possible they will become two separate species. This evolution of new species is called speciation. The factor that causes populations to separate is called an isolating mechanism. Endemism doesn't just occur between continents, it also occurs within them. For example, species can be restricted to large regions such as south-west Australia or tropical Queensland.
Endemism can also occur over very small areas, such as on mountain tops or around mound springs.
The isolating mechanism in both these cases would be the unsuitable nature of surrounding areas.