The protagonist mark is a gimmick introduced by Gaboza in Generation 3. It's a part of a character's design that gives away that they are the protagonist; though this mark changes with every new generation. For example, in Generation 3, this mark was an ahoge, which can be seen on all four of the mainline stories' protagonists.
Chloe's ahoge
Lexi's ahoge
Gio's ahoge
Benji's ahoge