Nine parishioners were killed last month when 21-year-old Dylann Roof shot attendees during a prayer group at the Emanuel African Methodist Episcopal Church in the US city of Charleston in South Carolina.
Since the shooting, eight African-American churches have been burned- three are believed to have been the result of arson, while the others are pending investigation.
In reponse to the shootings, Muslims charities have launched an online fundraising campaign for the churches, raising nearly $US27,000 ($A36,430).
In a statement the Muslim charities said "all houses of worship are sanctuaries, a place where all should feel safe, a place where we can seek refuge when the world is too much to bear.
"There has not been anywhere near the amount of resources needed to rebuild these churches. The time is now, let's unite to help our sisters and brothers in faith".
California-based imam and Muslim scholar Zaid Shakir added on his Facebook page that the fundraising campaign was a "small symbol of solidarity" between Muslims and African-American Christians.
"The American Muslim community cannot claim to have experienced anything close to the systematic and institutionalized racism and racist violence that has been visited upon African Americans," wrote.
"We do, however, understand the climate of racially inspired hate and bigotry that is being reignited in this country. We want to let our African American brothers and sisters know that we stand in solidarity with them during this dark hour."