The software company came under fire for appointing Eich as CEO last month. In 2008, he gave money to oppose the legalisation of gay marriage in California, a hot-button issue especially at a company that boasts about its policy of inclusiveness and diversity.
"We didn't act like you'd expect Mozilla to act," wrote Mozilla Executive Chairwoman Mitchell Baker in a blog post.
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The next step for Mozilla's leadership "is still being discussed," she added, with more information to come next week.
While gay activists applauded the move, many in the technology community lamented the departure of Eich, who invented the programming language Javascript and co-founded Mozilla.
"Brendan Eich is a good friend of 20 years, and has made a profound contribution to the Web and to the entire world," venture capitalist Marc Andreessen tweeted.
Eich donated $1,000 in 2008 in support of California's Proposition 8, which banned gay marriage in the state until it was struck down by the Supreme Court in June.
His resignation came days after OkCupid.com, the popular online dating site, called for a boycott of Mozilla Firefox to protest the world's No. 2 Web browser naming a gay marriage opponent as chief executive.
On Monday, OkCupid sent a message to visitors who accessed the website through Firefox, suggesting they use browsers such as Microsoft Corp's Internet Explorer or Google Inc's Chrome.
"Mozilla's new CEO, Brendan Eich, is an opponent of equal rights for gay couples," the message said. "We would therefore prefer that our users not use Mozilla software to access OkCupid."
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