The case, refiled on Monday by a prosecutor at the Court of Cassation, was initially sent back from the Constitutional Court in March on procedural grounds for lack of details.
The prosecutor's move in March was the culmination of a years-long crackdown on the HDP, parliament's third-largest party, under which thousands of its members were tried on mainly terrorism charges.
Pervin Buldan, co-leader of the HDP, said the judiciary should investigate recent allegations of corruption among top government officials rather than open a case against her party, Reuters reported.
"We can see the pit that the judiciary has fallen into," Buldan said, speaking to members of her party.
"The judiciary that cannot, does not come down on crime organisations has become a shield for the mafia order once again by launching a closure case against the HDP," she added.
Turkey has a long history of shutting down political parties seen as a threat and has in the past banned a series of other pro-Kurdish parties.
The latest indictment demanded a political ban on some 500 party members and a block on HDP's bank accounts, down from over 600 in the previous indictment, state-owned Anadolu agency said.
In a written statement, the prosecutor said the HDP committed crimes against the independence of the state and its unbreakable unity with its country and people.
Critics say Turkey's judiciary is under the influence of politics, a claim which the ruling AK Party and its Nationalist Movement Party (MHP) allies deny.
MHP leader Devlet Bahceli, who has repeatedly called for the closure of the HDP, said the Constitutional Court does not have the option to return the indictment a second time.
"This bloody and dark page should be closed never to be opened," Bahceli told members of his party on Tuesday.
Reporter's code: 50101