A change of leadership in Equatorial Guinea's federation saw president Andres Jorge Mbomio sack previous incumbent Andoni Goikoetxea last week.
With little time until the start of the tournament on January 17, the federation has moved quickly to appoint a successor, with Becker being given the nod.
The Argentinian had previously been in charge of the women's side - whom he led to glory in the 2012 African Women's Championship - and had been the country's technical director overseeing all teams.
Equatorial Guinea - who stepped in to stage the event after Morocco were stripped of the rights having requested a postponement due to safety fears over the spread of Ebola in the continent - will kick off the tournament and begin their Group A campaign against Congo, before further tests against Burkina Faso and Gabon.
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