Besides the seers, arraigned as accused 1 and accused 2 respectively in the murder of A Sankararaman, Manager of the Varadarajaperumal temple in Kancheepuram district, 21 other accused were also acquitted by Puducherry Principal District and Sessions Judge C S Murugan.
A total of 24 persons were made accused in the case, but one of them, Kathiravan, was killed early this year.
The judge held that the witnesses failed to support the prosecution case that the two Sankaracharyas - Jayendra (78) and Vijayendra (44) - were part of a conspiracy to eliminate the temple official in September 2004.
He also said the witnesses, including Sankararaman's daughter, failed to identify the accused in the court. None of them identified any accused in the court and no incriminating evidence was made out against the accused, the judge noted.
The arrest of Jayendra Saraswathi on Diwali day in November 2004 in Andhra Pradesh and later his heir apparent, Vijayendra, came as a big jolt to the Kanchi Mutt and its followers.
During the trial, 189 witnesses were examined between 2009 and 2012, of which 83 turned hostile. The keenly-anticipated judgement was delivered in a packed court hall for which security was beefed up in and around the area.
Sankararaman, who was murdered in his office room in the temple on September 3, 2004 using sharp-edged weapons, had levelled charges of financial misappropriation against the two Sankaracharyas and over the way they ran the Mutt.
Police from Vishnukanchi station took up investigation following a complaint and a case was registered under section 302 and 34 of Indian Penal code.
Cases were registered against the two seers under section 120-B (criminal conspiracy) and 302 (murder) of IPC in connection with the murder.

Reacting to the judgement, Sankararaman's son Anand said the verdict was "shocking and unbelievable" and wanted to know who were his father's killers. The family will go through the judgement and decide the next course of action including whether to appeal against the verdict, he said.
The seers' counsel said the prosecution had failed to prove the conspiracy charge and the witnesses, including Sankararaman's daughter Uma Maitreyi, had failed to identify the accused.
With no material or evidence "this is not a fit case for appeal," one of their counsel, K M Subramaniam, said. Lakshman Reddy, another of the seers' counsel, said no witness or documents were there to prove the involvement of the Sankaracharyas.
Earlier, it was alleged that the pontiff hatched a conspiracy to eliminate Sankararaman since he had allegedly made allegations against Jayendra Saraswathi. The others acquitted in the case include the Manager of the Mutt Sundaresa Iyer, junior pontiff Vijayendra Saraswthi's brother Raghu and KG Krishnaswamy alias Appu.
M Kathiravan, one of the accused, was killed in Chennai on March 21 this year. This brought down the number of accused in the Sankararaman murder case to 23 from 24.
The Special Investigation team of Tamil Nadu police filed the charge sheet naming Jayendra Saraswathi as first accused and Vijayendra Sarawathi as the second accused in the case.
The then District Superintendent of Police in Kancheepuram K Premkumar and the Superintendent of Police SP Sakthivelu who was the Chief Investigation Officer submitted the 1873-page charge sheet before the Judicial Magistrate (I) of Kancheepuram G Uthamaraj.
Jayendra Saraswathi was arrested on Diwali day on November 11, 2004 at Mahbub Nagar in Andhra Pradesh. After two months in jail in Vellore the seer was granted bail by the Supreme Court on January 10, 2005.
Vijayendra Saraswati was arrested from the mutt on January 10, 2005 and the Madras High Court granted him bail a month later. The Sankaracharyas moved the Supreme Court and got the case transferred to Puducherry in 2005 on the ground that the atmosphere in Tamil Nadu was vitiated and there would not be free and fair trial.
Ravi Subramanian, a civil contractor of the Mutt, who was among the accused, turned approver. He, however, later turned hostile during investigation in the case in Puducherry court on January 21, 2010.


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