The reigning champions, León, were eliminated in the quarterfinals by Irapuato on a 2–1 two-leg aggregate, and thus could not successfully defend their Clausura 2008 title.
Querétaro won the tournament, defeating Irapuato on a 2–0 two-leg aggregate, and will earn a spot into the promotional playoff held after the end of the Clausura 2009 season, where the winners of the two tournaments meet in an effort to gain promotion to the Primera División.
Instead, Irapuato were promoted to the Primera División A, and two new reserve teams were created for the Indios of Ciudad Juárez (Chihuahua) and Atlante (Chetumal).
If the two teams are tied after both legs in the quarterfinals and semifinals the higher seed advances automatically.
In the finals, if the two teams are tied after both legs two 15 minute halves of extra time are added.
In order for a team to be promoted it has to obtain a certification from the Federación Mexicana de Fútbol Asociación.
If the winner of the promotional final is not certified for promotion a home and home series is played between the highest placed certified team and the club being relegated to the Primera División A to determine which will be in the Primera División.
If the two teams are tied after both legs in the quarterfinals and semifinals the higher seed advances automatically.
In the finals, if the two teams are tied after both legs two 15 minute halves of extra time are added.
In order for a team to be promoted it has to obtain a certification from the Federación Mexicana de Fútbol Asociación.