Later he was a professor of missions and evangelism at Clear Creek Baptist Bible College.

Hughes' fiction tends to deal seriously with religious themes, particularly in The Fallen and its sequel The Eternity Gene.

Of his non-fiction, Satan's Whispers has the distinction of having been adopted for use by the Billy Graham Evangelistic Association.

Hughes' most extended body of work consists of his two fantasy sequences about a magical country split into three states by a two-headed dragon's occupation of the mountain pass linking each region with the others.

Hughes' powerfully imagined dragon Vicia-Heinox with its two bickering heads has set a pattern for the portrayal of similar creatures in other media, including the animated film Quest for Camelot (1998) and the public television children's program Dragon Tales (1999–2005).