Two paternal Sayyid lineages of him are currently known. From one line he is a direct descendant of the seventh Imam Musa al Kadhim, through his son Ibrahim al Murtadha and of the well known Sufi master Khwaja Sayyid Mir Alauddin Atar. Sayyid Alauddin Atar was the successor and son in law of Hazrat Bahauddin Naqshband. Therefore, Hazrat Ishaan is also from the progeny of Hazrat Bahauddin Naqshband, who was himself a descendant of the eleventh Imam Hasan al Askari, through his son Sayyid Ali Akbar. Hazrat Ishaan Saheb is also known to have a familiary relationship with the Sufi saintFarid ul-din Attar.
Hazrat Ishaan was the second son of Khwaja Sayyid Mir Sharif Naqshbandi. His older brother was Khwaja Khawand Muhammad Naqshbandi, known as Khwaja Khawand Aftab, who also was a saint. Hazrat Ishaan had issued 5 daughters and 6 sons, who are all regarded as saints.
Lineage
Registered lineages of him to the Prophet Muhammad, that are currently known are the following two: 1. Prophet Muhammad 2. Ali ibn Abi Talib and Fatima Al Zahra 3. Imam Hussain 4. Imam Ali Zayn al-Abidin 5. Imam Muhammad al Baqir 6. Imam Ja'far al-Sâdiq 7. Imam Musa al-Kazim 8. Imam Ali al Reza 9. Imam Muhammad al Taqi 10. Imam Ali al Hadi 11. Imam Hasan al-Askari 12. Mir Sayyid Ali Akbar 13. Sayyid Mir Mahmud Fakhriddin 14. Amir Sayyid Mir Muhyuddin 15. Amir Sayyid Mir Khalwati 16. Amir Sayyid Mir Naqi Naqib 17. Sayyid Mir Ilaq 18. Sayyid Mir Mahmud 19. Sayyid Burhan Qilchy 20. Sayyid Mir Shaaban 21. Sayyid Mir Qasim 22. Sayyid Mir Zayn ul Abedin 23. Sayyid Mir Abdullah 24. Sayyid Mir Burhanuddin Qilichiy 25. Amir Sayyid Mir Jalalludin Muhammad Bukhari 26. Amir Sayyid Burhanuddin Muhammad Bukhari 27. Hazrat Khwaja Sayyid Mir Bahauddin Naqshband 28. Shahe Naqshband´s daughter and her husband Khwaja Sayyid Mir Alauddin Attar 29. Hazrat Khwaja Sayyid Mir Hussain Atar Bukhari 30. Hazrat Khwaja Sayyid Mir Tajuddin Hussain 31. Hazrat Khwaja Sayyid Mir Muhammad 32. Hazrat Khwaja Sayyid Mir Zia ul Din 33. Hazrat Khwaja Sayyid Mir Sharif 34. Hazrat Khwaja Sayyid Mir Khawand Mahmud, also known as Hazrat Ishaan 1. Prophet Muhammad 2. Imam Ali ibn Abi Talib and Fatima Al Zahra 3. Imam Hussain 4. Imam Ali Zayn al-Abidin 5. Imam Muhammad al Baqir 6. Imam Ja'far al-Sâdiq 7. Imam Musa al-Kazim 8. Sayyid Mir Ibrahim 9. Sayyid Mir Abu Bakr al-Kabir 10. Sayyid Mir Abdul-Haq 11. Sayyid Mir Jafar 12. Sayyid Mir Muhammad Rumi 13. Sayyid Mir Abdullah 14. Sayyid Mir Musa 15. Sayyid Mir Hussein 16. Sayyid Mir Qasim 17. Sayyid Mir Abu Bakr Reza 18. Sayyid Mir Abdullah Zarbakhsh 19. Sayyid Mir Muhammad Khwarezmi 20. Khwaja Alauddin Attar 21. Hazrat Khwaja Sayyid Mir Hussain Atar Bukhari 22. Hazrat Khwaja Sayyid Mir Tajuddin Hussain 23. Hazrat Khwaja Sayyid Mir Muhammad 24. Hazrat Khwaja Sayyid Mir Zia ul Din 25. Hazrat Khwaja Sayyid Mir Sharif 26. Hazrat Khwaja Sayyid Mir Khawand Mahmud, also known as Hazrat Ishaan The significance of his lineage is an evidence for descendants of Imam Hasan al-Askari.
Spiritual journey
Hazrat Ishaan was influenced by his ancestors´ teachings and was therefore a disciple of his father. Hazat Ishaan was granted permission from his father to study in a royal college and had become an accomplished scholar. In the age of 23 years Hazrat Ishaan Shah Saheb has received a letter to visit his father and to accompany him in his last days. Upon his father, passing away, he has abandoned further studies and concentrated on the mystical quest. In this he first left to Wakhsh, where he has become Shaykh ul Islam, performing his duties there. While staying in Wakhsh, he got to know Khwaja Hajji. They have met a second time in Balkh, where Khwaja Hajji has introduced him to his future master Khwaja Ishaq Dahbidi and has become his disciple. He met him the second time in Bokhara and has become his disciple. After twelve years of spiritual training Hazrat Ishaan Saheb has reached the level of a Shaykh in Tasawuff in year 1598. Khwaja Ishaq Wali has welcomed him in his circle as the emperor of all Awliya Allah. On the order of Khwaja Ishaq Wali Hazrat Ishaan Saheb went to Lahore to propagate the Ishaqqiya path. Instead he went to Srinagar in Kashmir. In Srinagar he attracted many people, who have later followed him. The fame of his piety has reached many areas of Central Asia. Hundreds of thousands of disciples in Khorasan, modern-day Afghanistan, especially in the cities of Kandahar, Kabul and Herat, followed him. He has sent disciples in all over Central Asia under, whom 2 have been sent to Tibet. Unlike other Naqshbandi Masters he attracted many people, who were not only official patronages. Hazrat Khwaja Khawand Mahmud was invited by the Moghul Emperor Jahangir to go to his court in Agra. Going there several times, he was unable to create firm connections to the court, because of the influences of Naqshbandis attached to the rival Jubairiyya branch. Therefore, he came back to Kashmir. Becoming entangled in the struggle against the Shia community there, Moghul emperor Shah Jahan summoned him in year 1636 to Delhi and banned his way to Srinagar. Hazrat Ishaan spent his last six years in Lahore, where he also died.
Succession
Hazrat Ishaan was succeeded by his son Moinuddin Naqshabnd in Kashmir. His youngest son Bahauddin succeeded his father in Lahore in a very young age. His spiritual line died out in the late eighteenth century. Hazrat Ishaan has stated that one of his progeny will come to revive his lineage and to take his place as Ghawth. It has been found, that Hazrat Sayyid Mir Jan is this person, who is his successor in the Uwaisiyyah way.
Spiritual rank
Hazrat Ishaan was Qutb ul Aqtab, also called Ghawth, the highest ranking Wali Allah of his time. In Sufism the Ghawth is known as the cosmic leader of the whole universe and righteous successor of prophet Muhammad. It is said that Hazrat Ishaan stated that under his progeny there will come a son of him, who will revive the spiritual lineage and legacy of Hazrat Ishaan and who will take his place as Ghawth after him. His successor is Sayyid ul Sadaat Hazrat Sayyid Mir Jan.