PayPal was acquired by eBay in its early days in 2002, and the two firms have worked in partnership ever since.
The changes mean that while eBay buyers can still pay with PayPal, sellers will be paid straight into their bank accounts.
But some sellers have threatened to stop using the service over the move.
EBay's forums have several posts from sellers who say they are reluctant to use the new system and give eBay direct debit access to their personal bank accounts.
