Paramilitary Rangers arrested Qari Abdul Hayee, the former president of Lashkar-e-Jhangvi's (LeJ) Sindh chapter, during a raid in the city.
A source in the Rangers said that Hayee was wanted in several cases, including the murder of Pearl in 2002.
"He was first arrested in 2003 from Multan over his suspected involvement in planning and carrying out the kidnapping and murder of Pearl," the source said.
Hayee was also allegedly involved in helping another LEJ militant Riaz Basra escape from the Lahore sessions court in 1994.
The Rangers have been carrying out targeted operations in Pakistan's biggest city since a series of bomb blasts killed hundreds in Karachi and the provincial capital city of Baluchistan province, Quetta in January and March.
Both blasts targeted the minority Shia community killing more than 190 people. The LeJ had claimed responsibility for the Quetta blast and had threatened to exterminate all Shias.
Following the attack, LeJ leader Malik Ishaq and his son Malik Muhammad Usman were detained for a month.
Several other members of the banned outfit were also arrested during separate raids.
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