The rowdy group took every opportunity to disrupt proceedings.
While other delegates sang in welcome for the African National Congress leaders, the Gauteng group sat watching.
Mantashe was cheered by delegates from the Eastern Cape.
He arrived with ANC treasurer Zweli Mkhize. Deputy secretary general Jessie Duarte was also in attendance.
President Jacob Zuma was expected to address the conference later on Wednesday.
Earlier, the Gauteng group booed because they would not be allowed to elect new leadership at the conference.
On Tuesday, the ANCYL national task team had announced that the conference would no longer be an elective one but a consultative one.
Some delegates cheered as Congess of SA Students president Colin Malatji questioned why the conference was no longer to elect leaders.
“Our autonomy means we must have the right to convene our own meeting,” he said to cheers from delegates.
However, he called for delegates to be disciplined.
“You must be highly disciplined and call the ANC to guide us because it’s the ANC that guides our future.”
Delegates cut Malatji off and started singing and dancing.
A group from Gauteng picked up their chairs and raised them above their heads as they sang.
Water and Sanitation Minister Nomvula Mokonyane tried to get delegates to quiet down but to no avail.
She eventually called former ANCYL leaders Malusi Gigaba and Fikile Mbalula to greet the conference.
Gigaba was booed by some of the delegates while others cheered. Mbalula received a rousing welcome.
Mbalula warned delegates that the ANC would not “reward anarchy”.
“The ANC is under attack. We must defend the ANC,” he told delegates.
Mbalula asked that while the sessions were open delegates should treat the ANC leaders with respect.
“This congress will continue according to what the ANC wants.”