David Nelson and Nicole Anderson are each charged with three misdemeanor counts, including violation of civil rights, vandalism, and possession of tools to commit vandalism or graffiti, the district attorney's office said in a statement. The incident happened soon after the mural was painted in front of the courthouse in Martinez, California, on July 4.
"We must address the root and byproduct of systemic racism in our country. The Black Lives Matter movement is an important civil rights cause that deserves all of our attention," District Attorney Diana Becton said in a statement.
"The mural completed last weekend was a peaceful and powerful way to communicate the importance of Black lives in Contra Costa County and the country," she said. "We must continue to elevate discussions and actually listen to one another in an effort to heal our community and country."
When reached by phone by CNN, Nelson, 53, said "I have no comment -- for you anyway." CNN's attempts to reach Anderson, 42, went unanswered Tuesday night.
A woman, wearing a red T-shirt and flip-flops, began painting over the yellow-lettered mural with black paint Saturday, as seen in a video posted on YouTube and shared in a police statement. A man wearing a red Trump shirt that read "Four more years" began filming as the woman started painting.
"We're sick of this narrative, that's what's wrong," the man said in the video. "The narrative of police brutality, the narrative of oppression, the narrative of racism, it's a lie."
A bystander off camera can be heard arguing with the man. She asked what was wrong with him before adding, "This is racist, what you're doing."
Residents of Martinez got a permit from the city to paint a Black Lives Matter mural on July 4, Martinez Police Chief Manjit Sappal said in a statement.
Police had been looking for the man and woman seen in the video.
"It appeared that the couple came to the mural with cans of paint and a roller with the specific purpose of vandalizing over the mural," Sappal said in the statement. "The community spent a considerable amount of time painting this mural only to have the suspects destroy it by dumping and rolling paint over part of the message."
During the incident, the woman stopped painting to voice her concern, suggesting such murals be kept in New York. "This is not happening in my town," she said.
The mural was repainted after the incident, according to CNN affiliate KPIX. The area was blocked off and the mural was surrounded by chalk images as of Sunday afternoon, KPIX reported.
In an unrelated incident Sunday, a man was arrested for shouting "all lives matter" and pulling a gun on a young man looking at the same Black Lives Matter mural, according to CNN affiliate KGO.
Nelson and Anderson will be sent notices to appear in court. That date has not yet been released, according to DA spokesman Scott Alonso. If convicted of the misdemeanor charges, each defendant could face up to a year in county jail, according to the news release.
CNN's Cheri Mossburg contributed to this report.