People from both sides screamed at each other and threw water bottles, as the police tried to control the situation, firing pepper-balls.
The clash between pro and anti-Trump groups occurred after the Republican leader ended his speech in San Diego in the western California state yesterday, with several people throwing stones and plastic bottles, some that hit police officers.
After issuing orders to the crowd of roughly 1,000 to disperse, police began forcefully and aggressively pushing protesters - who were waving Mexican flags and holding anti-Trump signs - checking them with their batons. Some protestors also scaled barriers, according to reports.
At least 35 people were arrested, police said, adding that no property damage was reported and no injuries were reported.
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"Crowd behaviour has become unlawful. An unlawful assembly has now been declared. It is illegal to remain in the area," the San Diego Police said in a situational update, adding its forces would be deployed till late in the night.
At his rally, Trump also responded to US President Barack Obama's comments a day ago that world leaders are rattled by his campaign rhetoric and assured his supporters that he would get along well with foreign leaders.
"I happen to be a nice person, folks. I'll get along great. I will get along so great with these countries. I will get along so great," Trump told thousands of his supporters.
Someone grabbed a man's "Make America Great Again" hat and burned it, according to San Diego Tribune.
Officers in helmets, masks, pads and with long wooden batons massed in lines, then moved slowly toward the unruly protesters. By evening, police had managed to move and disperse the crowd, and few were left, the daily reported.
Trump was in the city near the Mexican border to hold a rally ahead of the 7 June California primary and in his San Diego rally pledged to build a border wall to keep out illegal immigrants.
Earlier yesterday in Fresno, Trump denied that there was a major drought affecting the state, saying instead that when he becomes president he will "start opening up the water".
"Great rally in Fresno, California- great crowd! Thank you!" he said in another tweet.
At the San Diego rally, Trump said the US under his presidency would start winning again.
"Every single country no matter what -- name a country -- we lose. We don't win anymore. We're going to start winning. We're going to win with trade. We're going to win with our military. We're going to start winning again," he said amidst applause.
"Then you look at the NATO countries -- 28 total, many of them aren't living up to their obligations," he said. "They have been abusing us. They have been abusing us. This isn't 40 years ago when we could have done whatever we want."
Continuing with his criticism of Hillary Clinton, Trump said the Democratic presidential frontrunner and former secretary of state is a "very boring" speaker.
"I watched Hillary Clinton last night, which was hard to do because she's a very boring speaker," he said.
"But I found it very hard to watch. And then she lies. Now, you know, I called somebody a liar, but I don't say that anymore because that person is now in the past. I say that person is in the past. And with Hillary, we say "Crooked Hillary," he said.
"But I've got to add another word because I never saw anything like this last night. She was saying that "I want Japan to arm with nuclear weapons." I never said that. She was saying, "I love the dictator in North Korea." I don't love the dictator -- bad guy, OK? Bad guy.
"Take a look at what's going on with our military that we love. We can't beat ISIS. We're going to beat ISIS. We're going to beat them quickly. We're going to knock the hell out of them. We shouldn't have been there in the first place, but we're going to knock the hell out of them. And we have to rebuild our country," he said.