Marzouki, a fierce opponent of ousted dictator Zine El Abidine Ben Ali, formally presented his candidacy at the offices of the electoral authority, watched by journalists.
"I trust the intelligence of the Tunisian people to know who is able to serve," the 69-year-old secular leader told reporters.
Marzouki became Tunisia's first elected president in December 2011, following a vote in the constituent assembly.
It came 11 months after the ouster of Ben Ali that triggered the Arab Spring, which also swept away long-time dictators in Egypt and Libya.
But after months of wrangling, political parties agreed a deal in June to end the crisis.
After months of negotiations, parliamentary and presidential elections were approved for October 26 and November 23, respectively.
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