The columns of protesters, carrying umbrellas against steady rain and some wearing the colours of the Philippine flag, chanted "Duterte is afraid of women" as they wound through city streets.
During two years in office, Duterte has repeatedly and unapologetically joked about rape, defended womanising and ordered soldiers to shoot women rebels in the vagina.
Last week he sparked outrage after coaxing a married Filipina into kissing him on the lips onstage during an appearance in Seoul, which he defended by saying "We enjoyed it".
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"We are saying we have had enough," activist Jean Enriquez told AFP as she marched. "All the acts of the Duterte administration and he himself contributed to us, the women, coming out."
Enriquez is part of a collective of women who launched last month a #Metoo-style social media campaign that takes aim at Duterte's attitude towards women.
Their #BabaeAko (I am a woman) hashtag caught on quickly in the social media-obsessed nation, and the thousands of posts since were the catalyst for Tuesday's independence day rally.
Organisers and an AFP journalist estimated that about 1,500 people, including men, took part in the march.
The #BabaeAko co-founders launched the campaign in outrage after Duterte said the nation's next chief justice would be someone with "integrity", "especially not a woman".
"A woman is not an object... Grow up and start treating women how they deserve to be treated #BabaeAko", said broadcast journalist Kara David in a tweet that had been shared a thousand times.
Twitter user @piecesofchi posted, "I am a single mother, struggling to support my family while quietly but steadfastly pursuing my dream. #BabaeAko and nobody is allowed to diminish my worth."
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A former mayor who cultivates a man-of-the-people image, the 73-year-old Duterte has regularly fought with women in powerful posts who dared to oppose him.
His top critic, Senator Leila de Lima, is being held on drug charges she insists are politically motivated.
While the first female head of the nation's top court, Maria Lourdes Sereno, was ousted last month by her Supreme Court colleagues after questioning Duterte's deadly crackdown on narcotics.
During his 2016 campaign for president Duterte set the tone by telling a crowd about a 1989 prison riot in the southern city of Davao where he was mayor.
"There was this Australian lay minister... They raped her, they all lined up. I was mad she was raped but she was so beautiful. I thought, the mayor should have been first.'"
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