Brin and Anne Wojcicki, who married in 2007, have been living apart for several months, the couple's spokesperson said.
"They remain good friends and partners," the spokesperson added.
The technology blog AllThingsD on Wednesday was the first to report of the couple's living apart. Brin and Wojcicki, who have two children and who have a prenuptial agreement, are not yet legally separated, the report said.
Susan Wojcicki, Anne's sister, is Senior Vice President of Ads and Commerce for Google and is considered one of the Internet company's top executives.
The relationship between Google and the Wojcickis dates back to the company's earliest days: in 1998, the nascent search company set up shop in Susan Wojcicki's garage shortly after raising its first funding.
Google has invested roughly $10 million in 23andMe, the company that Anne Wojcicki co-founded in 2006 and which maps DNA and provides clients with information about their ancestry.
© Thomson Reuters 2013