The Los Angeles and Long Beach ports will begin charging a $15 fee on all loaded cargo containers in 2009 as part of a multi-billion-dollar plan to fund local transportation projects.

Both ports on Monday approved the fee the second in the past month to generate more than $1.4 billion over the next seven years. The ports plan to obtain matching funds from the Proposition 1B infrastructure bonds approved by California voters in 2006.

The funds will be used for highway, rail and bridge projects around San Pedro Bay, including an overhaul of the Gerald Desmond Bridge.

The fee was applauded by Los Angeles Mayor Antonio Villaraigosa, who has pressured the ports to reduce the amount of pollution it generates while preparing for an expected surge in cargo capacity in the coming years.

“This fee is essential to the ports’ progress in cutting the amount of traffic congestion and diesel pollution at the Ports,” said Villaraigosa in a statement Monday. “It’s critical we meet the expected burst of trade at the ports with smart, effective planning and green growth now.”

The tax comes just weeks after the ports approved a $35 cargo fee that will generate more than $1.6 billion to finance its controversial truck replacement program. As part of their sweeping clean air program, the ports plan to replace nearly all of the estimated 16,000 short-haul diesel trucks in the harbor with new, cleaner models.