Although he is not affiliated to the Al Qaeda as Musa was, Naikoo is the most senior commander of the pro-Pakistan Hizbul Mujahideen or HM, to which Musa too belonged until he got tired of the group and dumped it.
And like Musa, Naikoo too hails from Pulwama district but from Awantipora area.
A major blow was dealt to militancy in Kashmir by the security forces when they eliminated Musa. Police sources admit a successor to Musa would not be easy for the militants to find.
Musa grew in stature after he succeeded Burhan Wani as the commander of the HM. Burhan was killed on July 8, 2016.
The militancy's poster boy image fitted Musa rather well.
As Burhan's friend, his acceptance was easy for the HM militants who desperately needed a young man to keep on the recruitment of local educated youth belonging to well-to-do families.
But Zakir got disgruntled with the HM. He was then declared the chief of Al Qaeda affiliate, Ansar Ghazwatul Hind.
A post graduate in mathematics and tech savvy, Naikoo took over the command of the HM after Musa quit.
He quickly became the second most wanted militant commander in the Kashmir Valley.
Categorised as "A++" level militant, intelligence agencies believe Naikoo is more of a 'liberal militant commander' as compared to Musa who settled for nothing except the struggle to establish an Islamic state in Kashmir.
Naikoo's appearances at funerals of slain militants where he would offer gun salutes became a major problem for the security forces.
"These so-called gun salutes were actually recruitment rallies by the militants and Naikoo spearheaded the campaign well for the HM," said an intelligence officer.
Abductions of families of policemen attributed to Naikoo forced the police brass during 2016-17 to tell policemen not to visit their families in south Kashmir areas without security and permission from seniors.
This threat become more real by circulation of Naikoo's threatening video clips on the social media.
He warned youths to stay away from Army recruitment rallies, goodwill functions and other events organised by the security forces to prevent them from joining the militant ranks.
It needs to be seen whether Naikoo's image as an insurgent of home-grown militancy survives after Musa or not.
( With inputs from IANS )