Philips - who joined the programme's production team last year - will work alongside executive producers Carolyn Reynolds and Tony Wood as Hollyoaks undergoes further transformation in the year ahead.
Speaking of his new role, Philips commented: "I have really enjoyed working in the script team at Hollyoaks and it will be a huge honour to take the reins of Channel 4's flagship youth drama.
"I am very excited about taking the show even further this year with more compelling and brave stories."
Marquess, meanwhile, is leaving the role of series producer at Hollyoaks but will continue to work with production company Lime Pictures on a number of other shows.
In a statement, Marquess said: "When I agreed to give up my life for a year to run a soap again, I never thought it would fly by so quickly. It's now the right time to hand over Hollyoaks and I'm looking forward to new projects."
Since replacing Lucy Allan in January 2010, Marquess has instigated a number of changes at the teen soap, writing out several characters and unveiling new signings to take their places, including Sheree Murphy (Eva Strong), Kim Tiddy (Heidi Costello), Emmett Scanlan (Brendan Brady), Alex Fletcher (Diane O'Connor) and Stephanie Davis (Sinead O'Connor).
Ste and Brendan's dark relationship, Jasmine's transgender struggle, the devastating Il Gnosh fire and a new serial killer plot are among the storylines which have been overseen by Marquess.
Discussing the changeover, Carolyn Reynolds said: "I'd like to thank Paul Marquess for all he has done for Hollyoaks in the last 12 months. It's been great working with him again and we look forward to embarking on new projects.
"We're also delighted to be working with Gareth Philips. He's a very talented storyteller and this is a very exciting appointment for Hollyoaks." Get the Inside Soap magazine on your iPhone or iPad