The Council on American Islamic Relations (CAIR) said worshipers at the Islamic School of Miami discovered obscene graffiti on Thursday night on the school's sign.
Vandals wrote an explicit insult and scrawled a Nazi swastika on the exterior sign of the centre. Authorities were investigating the case.
CAIR was also investigating reports of vandalism at another Miami Islamic centre. Officials with Masjid al-Ihsan say their mosque was broken into and damaged.
Representatives of a third Islamic centre in Hollywood, Florida, reported to CAIR they received an anti-Muslim message in the centre's mailbox.
There are about 40,000 Muslims in the Miami area.
Several incidents targeting mosques and Islamic centres have occurred recently across the US.
CAIR, America's largest Islamic civil liberties group, has warned of rising anti-Muslim sentiment in the US after the 11 September 2001 attacks and in the wake of the Iraq war.
In an attempt to counter Islamophobia, CAIR has launched an online petition and published newspaper articles to tackle "misperceptions of Islam".
The petition, called Not in my Name, follows the brutal murder of a US hostage by a group in Iraq allegedly linked to al-Qaida.
CAIR, which condemned the apparent beheading of Nicholas Berg last week, says ordinary Muslims should not be blamed for "the un-Islamic and barbaric deeds of a minuscule minority".