From above link.
Terrorist and Extremist Groups of Pakistan
Terrorist Groups
Extremist Groups
Domestic Organisations
Lashkar-e-Omar (LeO)
Sipah-e-Sahaba Pakistan (SSP)
Tehreek-e-Jaferia Pakistan (TJP)
Tehreek-e-Nafaz-e-Shariat-e-Mohammadi
Lashkar-eJhangvi (LeJ)
Sipah-e-Muhammad Pakistan (SMP)
Muttahidda Quami Movement - Altaf Hussain (MQM)
Haqiqi Muhajir Quami Movement (MQM-H)
Baluch People's Libration Feont (BPLF)
Baluch Students' Organistaion (BSO)
Jamaat-ul-Fuqra
Nadeem Commando
Popular Front for Armed Resistance
Muslim United Army
Harkat-ul-Mujahideen Al-alami
Baluch Students' Organistaion - Awami (BSO-A)
Trans-national Organisations
Hizb-ul-Mujahideen (HM)
Harkat-ul-Ansar (HuA, presently known as Harkat-ul Mujahideen)
Lashkar-e-Toiba (LeT)
Jaish-e-Mohammad Mujahideen E-Tanzeem (JeM)
Harkat-ul Mujahideen (HuM, previously known as Harkat-ul-Ansar)
Al Badr
Jamait-ul-Mujahideen (JuM)
Lashkar-e-Jabbar (LeJ)
Harkat-ul-Jehad-i-Islami
Muttahida Jehad Council (MJC)
Al Barq
Tehrik-ul-Mujahideen
Al Jehad
Jammu & Kashir National Liberation Army
People’s League
Muslim Janbaz Force
Kashmir Jehad Force
Al Jehad Force (combines Muslim Janbaz Force and Kashmir Jehad Force)
Al Umar Mujahideen
Mahaz-e-Azadi
Islami Jamaat-e-Tulba
Jammu & Kashmir Students Liberation Front
Ikhwan-ul-Mujahideen
Islamic Students League
Tehrik-e-Hurriat-e-Kashmir
Tehrik-e-Nifaz-e-Fiqar Jafaria
Al Mustafa Liberation Fighters
Tehrik-e-Jehad-e-Islami
Muslim Mujahideen
Al Mujahid Force
Tehrik-e-Jehad
Islami Inquilabi Mahaz
Al-Rashid Trust
Al-Akhtar Trust
Rabita Trust
Ummah Tamir-e-Nau