Thousands of people marched through the city of Tacloban as sirens sounded and bells rang at the exact time the storm hit.
There were also anti-government protests at what some see as the slow pace of rebuilding.
President Benigno Aquino has denied moving too slowly. More than 7,000 people were killed in the disaster.
Typhoon Haiyan, known as Yolanda in the Philippines, hit on November 8 2013, sending huge storm swells into inland areas and destroying wide swathes of central Philippines.
More than four million people were displaced, many of whom are still living in temporary shelters.
Ceremonies were held on November 8 at mass graves in Tacloban where several thousand victims of the storm are buried.
Thousands marched by candlelight through the city at dawn, passing through areas devastated by the typhoon.
Gathering at the graves, mourners wrote names of loved ones on white crosses planted symbolically to represent unidentified victims.
“It’s important that we make it meaningful, so for the next generation’s people will remember this,” city mayor Alfred Romualdez said, quoted by Reuters news agency.
Hundreds also staged protests in the city and in the capital Manila at what they regard as a lack of progress in reconstruction.
The protesters burned an effigy of the president in the middle of Tacloban.
President Benigno Aquino has been accused of showing a lack of urgency in the reconstruction, with plans to find safe land away from the coast and build new homes falling behind schedule.
Benigno Aquino says the plan will take time.
“I would hope we can move even faster and I will push everybody to move even faster, but the sad reality is the scope of work you need to do can really not be done overnight,” said the president.
The president has decided not to come here to mark the anniversary, although he visited the typhoon-hit Eastern Samar province on November 7.
Tacloban is a stronghold of Benigno Aquino’s political enemies – it is the birthplace of former First Lady, Imelda Marcos.
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