Marquess took the helm at the Channel 4 teen soap at the beginning of the year, replacing Lucy Allan after her 12-month tenure. Kirkwood was handed the keys to his new office on March 1 when Diederick Santer stepped down from his role as executive producer after three and a half years.
Of Kirkwood, who enjoyed a successful three-year run helming Hollyoaks, Marquess told Radio Times: "I have high hopes for Bryan at EastEnders. Traditionally, that job was seen as a staging post on a BBC career - 'Come and do EastEnders for a bit, darling!' - but Bryan's appointment is an acknowledgement that the show is about the audience."
He continued: "If any show can reinvent itself, it's one that is concerned with rites of passage and is so focused in terms of its audience."
While numerous Hollyoaks cast members have already fallen by the wayside, Marquess recently revealed a raft of new signings.
Marquess added: "The adults are key to Hollyoaks - you'll be seeing a lot more of Frankie and Jack, say - but we want to tell stories from the point of view of our young characters."