Beginning in the 1990s, Merlis published a series of novels. His first novel, American Studies, was published in 1994Nishant Shahani, "The Politics of Queer Time: Retro-Sexual Returns to the Primal Scene of American Studies". Modern Fiction Studies, Vol. 54 Issue 4 (Winter 2008). p791-814. and won the Ferro-Grumley Award for LGBT Literature and the Los Angeles Times Book Prize Art Seidenbaum Award for First Fiction in 1995, and his second, An Arrow's Flight, was published in 1998"Merlis, Mark. An Arrow's Flight". Library Journal, August 1998. pp. 132-133. and won the 1999 Lambda Literary Award for Gay Fiction. He published two further novels during his lifetime, Man About Town in 2003"Mark Merlis' new novel hits closer to home". Philadelphia Gay News, July 4, 2003. and JD in 2015."A Married Man in the ’60s". The Gay & Lesbian Review Worldwide, May 1, 2015.
