n 18 May 2007, nine people were killed and 58 wounded in the blast during the Friday prayers in the Mecca Mosque.
Judge Rabindra Reddy gave the verdict on Monday afternoon after 11 years of long.
In the verdict, he said that the National Anti-Terrorism Agency (NIA), India's top anti-terrorism agency, could not prove anybody's crime. Everyone is being acquitted due to lack of evidence.
After a few hours, he announced his resignation for personal reasons and said NDTV.
Although the NIA failed to prove the crime, the former member of the Hindu nationalist right-wing group Rashtriya Swayamsewak Sangha (RSS), Swami Aasimanand, admitted that the bomb was involved in the bombing.
He also gave written confession about this.
After the local police investigation in Hyderabad, the case was handed over to the CBI. After the incident investigation, the CBI submitted the charge sheet.
NIA took charge of the case from the CBI in 2011.
The complaint was made in connection with 10 members of the RSS involved in the attack on the mosque.
Besides husband Asimananda, Debendra Gupta, Lokesh Sharma, Bharat Mohanlal Rateshwar alias Bharat Bhai and Rajendra Chaudhary face trial.
Two other accused Sandeep V Donghe and Ramchandra Kalsangra, who were accused during the trial, disappeared and the other accused Sunil Joshi died.
A total of 226 witnesses testified and nearly 411 documents were displayed.
During the trial, Swami Asimanand and Bharat Mohanlal Rateshwar were in jail and the other three were held in Central Jail in Hyderabad.
In March last year, Asimananda was acquitted of Ajmo blast case.
After the verdict on Monday, Hyderabad lawmaker Asaduddin Owaisi raised the question about the verdict, saying it is a 'mischief'.