Its initial brief is understood to be to move the brand slightly more upmarket.
Beattie McGuinness Bungay resigned the account in January after its was hired to work on Express Newspapers' Daily Star. Zoo launched in 2004 with a campaign through NMI.
Emap's head of marketing for men's magazines, Nial Ferguson, said: "We feel Mother fits with the direction Zoo is moving in under Anthony Noguera."
Zoo 's most recent Audit Bureau of Circulations figure, in August last year, saw an 8.4 per cent rise in circulation. It is widely predicted to be looking at 10 per cent growth in the next ABCs, due in mid-February.