Anthony Noguera, the editor of Arena and a former FHM editor, will take over the responsibility for Zoo in the UK from Merrill.
As the editor-in-chief of Emap's men's lifestyle portfolio, Noguera will also retain his responsibility for Arena.
Merrill has been Zoo's editor since its launch in January last year.
He will take up his new role as the international editor later this month.
He will focus on the launch of Zoo in Spain initially, which takes place this week. Emap has not signed any other licensing agreements, but it is investigating new markets.
Emap will hope that Zoo can ape the international success of FHM. The title now has 30 editions worldwide and FHM has become an Emap division in its own right.
Philip Thomas, the managing director of Emap East, said: "With Anthony and Paul in their new roles, we will be in a strong position to be able to build on the successes we have had so far."
Merrill added: "Editing Zoo has been an amazing experience and making it a global brand was always the logical next step."
In the UK, Zoo is still trailing its IPC Media rival, Nuts. However, in the latest ABCs, the Emap title was gaining on Nuts with a 20 per cent increase in circulation to 240,215 copies. Nuts has an ABC figure of 275,459.