Organic, which counts Bank of America and Chrysler as clients, does not have a replacement for him lined up, but a steering committee is in place to search for a new CEO.
"[Mark] has accomplished what he's needed to accomplish," said Amanda Van Nuys, an agency spokeswoman. "He's leaving the company in a good position."
Mr. Kingdon has worked as CEO of Organic since 2001. Prior to joining the agency, he was a partner with the consulting division of Pricewaterhouse Coopers.
Mr. Kingdon could not immediately be reached for comment.
Second Life, a virtual world, was a hotspot for marketers last year, but seems to have lost some of its luster this year. Philip Rosedale, founder of Linden Lab and the chairman of the company, in a statement said Mr. Kingdon's "management style, unwavering leadership in the face of great challenges, and approach to team-building exactly matches Linden's needs."
Mr. Rosedale announced he was stepping down as the CEO of Linden Lab earlier this year.