A man entered the Islamic Center on Eckstrom Avenue two months ago ranting against its members and calling them "terrorist rats."
A Muslim civil rights group said anti-Muslim groups are spending millions of dollars to spread fear and hate about Islam.
The Council on American-Islamic Relations (CAIR) identified 37 organizations it claims have an anti-Muslim agenda in the report "Legislating Fear: Islamophobia and its impact in the United States."
The Council says those groups had a total budget of $120 million to spread their message.
San Diego-area director Hanif Mohebi says messages of fear and hatred caused violent acts, including physical attacks on more than fifty mosques, in the U.S
"There are certain cases that we have, where people will snap out and unfortunately do very hateful things," Mohebi said.
The Council says Californians are more tolerant of Islam, compared to many other Americans.
Even so, the group says prejudice against Muslims in San Diego is a big problem.
The report cites at least 80 cases of alleged discrimination against Muslims, in San Diego, last year.
"Our office has received last year about 70 cases of discrimination. This year actually we already have over 80. So unfortunately on a local level it's going up," Mohebi.
In July, a man threatened a San Diego Mosque, and its Islamic school.
"Threatens to kill people, during one of the prayers, early morning prayers. He's arrested, and that came after almost three months of threats to the school, of bombing,” Mohebi said.
Fifty-two-year old Larry Rodgers was arrested after members of the mosque confronted him.
The report lists what it considered its "worst list" including the home improvement retail chain Lowe's which pulled its advertising from the reality show "All-American Muslim" in 2011.
As part of its report, the Muslim-American group thanked Americans who have pushed-back against discrimination including New Jersey Governor Chris Christie, and Illinois Senator Dick Durban.