The move against the two-term mayor caps a months-long legal crackdown on opposition figures across the country which has been criticised as a politicised attempt to hurt their electoral prospects.
Turkey's lira currency crashed as much as 12% to an all-time low of 42 to the dollar in response, underscoring worries over the eroding rule of law in the major emerging market and NATO member country that Erdogan has run for 22 years.
Imamoglu, 54, who leads Erdogan in some opinion polls, was to be named his Republican People's Party's (CHP) official presidential candidate within days. He now faces two separate investigations that also include charges of leading a crime organisation, bribery and tender rigging.