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Gillingham were torn apart by Bolton for the second time this season.
Bolton, who beat the Gills 4-0 in December, dominated the opening half at Priestfield and scored with three headers.
Josh Vela made it 4-0 early in the second half to match the previous scoreline.
Reaction: Boss sticks up for players after heavy loss
Gills boss Adrian Pennock made two changes to the team which beat Scunthorpe at the weekend, both enforced.
Penalty-hero Josh Wright missed out through suspension while Chris Herd failed to recover from a knee injury in time. Ollie Muldoon came in for his first start under Pennock and Jake Hessenthaler made a return to the XI.
Bolton were a class above the Gills in their last meeting and they arrived at Priestfield buoyed by a 4-2 win over fellow promotion chasers Fleetwood.
Once again Bolton turned it on and found it easy against a Gills side who were outfought from the off.
Bolton had their opening goal after just three minutes and it was a simple header for defender David Wheater. He nodded home unchallenged from a Filipe Morais corner.
Gillingham hadn’t got out of their own half before conceding the first goal and soon found themselves two down. Morais was again the provider and Le Fondre this time took advantage of slack marking, with 15 minutes gone, to head in from close range.
Chances for the Gills were rare. Joe Quigley fired an effort well over and their only on-target of the half was a low struck free-kick from Bradley Dack that was comfortably gathered by keeper Ben Alnwick.
Gillingham might have had a glimmer of hope at 2-0 but a third came in first-half stoppage time. It was déjà-vu. A Morais cross and a headed goal, this time Mark Beevers getting in on the act.
The Gills switched to a diamond in midfield for the second half but within four minutes of the restart Bolton had a fourth. Morais – a free transfer signing from Bradford - once again provided the assist. His low cross was met by Josh Vela and he found the net.
A good save from Stuart Nelson denied Darren Pratley from close-range but the visitors eventually took their foot off the gas and coasted home for the three points.
Gillingham (3-5-2): Nelson, Ehmer, Oshilaja, Rehman, Hessenthaler, Byrne, Muldoon, Martin (Osadebe 87mins), Dack, McDonald (List 87mins), Quigley (Parker 61mins). Subs not used: Holy, Dickenson, Cundle, Mbo.
Bolton (3-5-2): Alnwick, Dervite, Beevers, Wheater, Morais (Henry 84mins), Taylor, Pratley (Karacan 71mins), Osede, Vela, Le Fondre, Madine (Clayton 78mins). Subs not used: Howard, Moxey, Trotter, Long.
Attendance: 5,199 (517 away)