Ninety-six Liverpool fans were killed in a crush at the start of the FA Cup Semi Final between Liverpool and Nottingham Forest in 1989.
3.06pm marks the time the referee stopped the match after police became aware that fans were being crushed at the front of the Leppings Lane end of the stadium.
Thousands of fans gathered at Anfield Stadium for a memorial service at 2.45pm, while public transport ground to a halt across the city for the two minute silence.
Church leaders were among those present at a service of remembrance in Sefton, Liverpool, home to 18 of the victims.
The service was joined by the Deputy Mayor of Sefton, Cllr Alf Doran, who delivered a short address before prayers were offered by local church leaders, reports the Southport Visiter.
Church bells rang out across Liverpool at 3.06pm and in Sefton, a bell was rung 96 times.
Cllr Alf Doran said: “By marking the 20th anniversary in Sefton, along with all the other Hillsborough remembrance events taking place, this acts as a clear symbol that we will never forget the 96 Liverpool fans who died."
