The midfielder has been a regular starter for Millwall in recent seasons, but new boss Ian Holloway appears to be seeking fresh faces in the first-team and has allowed Trotter to join their Championship rivals.
A statement on Bolton's website read: "Bolton Wanderers can announce the signing of Liam Trotter from Millwall on loan for the remainder of the 2013/14 season.
"The 25-year-old has been handed shirt number 17 and subject to clearance he is eligible to play in Saturday's league game away at Ipswich Town."
Trotter is the second deadline day arrival at Bolton as Yannick Bastos earlier joined from Luxembourg side FC Differdange 03, for an undisclosed fee.
The 20-year-old winger signed a deal until June 2015 and will link-up with the club's development squad.
Bastos said: "I am really happy to be in Bolton. It is a dream that really came true and I am very proud to be here."