The Lawrence Family Jewish Community Center received a threat early Tuesday, San Diego police confirmed.
A security guard at the facility on Executive Drive called police to report a threat at the building just after 6 a.m.
It's not known what type of threat or how the threat was received.
The Lawrence Family Jewish Community Center is one of dozens of Jewish Community Centers in at least 20 states targeted since the new year began.
The FBI said it is joining with the Justice Department's Civil Rights Division to investigate "possible civil rights violations in connection with threats" to Jewish centers across the country.
On Tuesday, Hillary Clinton called a series of threats and attacks against Jews and Jewish groups "so troubling" in a tweet Monday and urged President Donald Trump to speak out against them.
Trump did so over an hour later, saying a series of bomb threats to Jewish community centers around the country "are horrible and painful and a very sad reminder of the work that still must be done to root out hate and prejudice and evil."
San Diego police responded and evacuated the building as a precaution.
They searched the building and are on scene to continue their investigation.
As of 7:30 a.m., the building was reopened.