Google co-founder Sergey Brin and wife, Anne Wojcicki, separate

In a high-profile Silicon Valley split that comes amid reports of a complicated office romance, Google (GOOG) co-founder Sergey Brin has separated from his wife, biotech entrepreneur Anne Wojcicki.

The surprising development was not widely known until Wednesday, but a representative for the couple confirmed to this newspaper: “Anne and Sergey have been living apart for several months. They remain good friends and partners.” The couple has two children and until recently lived in Los Altos Hills.

Brin and Wojcicki, both 40, are highly influential figures in the tech industry and also rank among Silicon Valley’s biggest donors to charity. Brin is one of the world’s wealthiest men and, with Google co-founder Larry Page, one of two controlling shareholders in the giant Internet company.

While there was no explanation for the split and neither has filed for divorce, the tech blog All Things D, which first revealed the separation, reported that unnamed sources said Brin is romantically involved with an unidentified Google employee.

In another twist, the blog reported late Wednesday that a senior Google executive, who previously dated the person Brin is now seeing, is leaving the company. But All Things D said its sources insist that Android vice president Hugo Barra’s departure for a new job is unrelated to Brin’s new relationship.

Brin’s vast stake in Google may not be at risk in the breakup, according to sources, because the couple signed a prenuptial agreement before they married in 2007 — at a low-profile ceremony in the Bahamas where both bride and groom reportedly wore swimsuits.

But the split could lead to some awkward moments in one of Google’s many cafeterias. Anne Wojcicki’s sister, Susan Wojcicki, is a longtime Google employee who now holds a top leadership position as senior vice president for advertising and commerce. Susan Wojcicki rented part of her Menlo Park home to Brin and Page when they first started Google, and according to Silicon Valley legend, she later introduced Brin to her sister Anne.

A Google spokesman did not respond to a request for comment Wednesday.

Anne Wojcicki is co-founder and CEO of a biotech startup, 23andMe, which sells personal DNA test kits and provides reports on individuals’ genetic makeup, traits and health conditions. Brin and Google are among the company’s major financial backers. A spokeswoman for 23andMe declined to comment Wednesday.

Brin, meanwhile, has left most of the executive responsibilities at Google to his longtime friend and co-founder, Page, the company’s CEO. But he is an extremely influential figure in the company, often vetting new projects and overseeing Google X, the division responsible for some of Google’s highest-profile “moonshot” efforts, including its self-driving cars and Glass, a wearable computer.

Like Page, Brin is paid only a $1 a year by Google. But he controls nearly 28 percent of the voting shares in the company and has a personal fortune worth more than $20 billion.

As a couple, Wojcicki and Brin were ranked among the five biggest donors to U.S. charities in 2012, after giving away $223 million last year. Their Brin Wojcicki Foundation supports human rights and anti-poverty programs, and the couple also has donated to research into Parkinson’s disease.

They also helped launch a major science foundation, which awards the Breakthrough Prize in Life Sciences, earlier this year along with Facebook’s Mark Zuckerberg, his wife Priscilla Chan, and other tech figures.

Mercury News staff writer Dan Nakaso contributed to this report. Contact Brandon Bailey at 408-920-5022; follow him at Twitter.com/BrandonBailey.