The term "Bunker" refers to the fuel that is used to operate ships. Bunkering is the action of supplying a ship with bunkers. The ship operator is responsible for the payment of these bunkers to the bunker supplier.
As fuel prices are quite volatile, the shipping lines charge a fee called "Bunker Adjustment Factor (BAF)" to cover the fluctuations in global bunker costs.
This BAF is charged either as a separate charge or included in the freight charge depending on the trade route.