The 2.1 meters-tall center played for New Zealand in the past two Olimpics.
He played 23 games for the Spurs last season missing the first 42 games with a sprained back and another 13 with a sprained left foot.
"Sean is important to the chemistry of our team," said coach Gregg Popovich. "We're thrilled to have him back."
Marks, 30, had a season-best 10 rebounds against the Los Angeles Clippers on April 6 but was not included on San Antonio's playoff roster.
The Spurs will seek their fourth title in eight years in the upcoming season after defeating Detroit in seven games in June's NBA Finals.
A six-year NBA veteran, Marks was selected by the New York Knicks in the 1998 NBA Draft and has also played with Toronto and Miami.
» Familiar Names Kick Off The New NBA Season
» Tim Duncan Brings The San Antonio Spurs To Life
» Steve Francis Leaves Behind Magic For Knicks
» Ray Shero Decides Keeping Center Jordan Staal
» A.J. Burnett Fired By Marlins
» McKie Agrees To Two-Year Contract With Lakers
» Video-gaming Improves Surgeons' Skills
» Lampard Admites That Sven Was Right