Firefighters said they found heavy fire and smoke coming from the sanctuary of South Union Missionary Baptist Church, which is on Lydia Street near Tierwester Street, just before midnight.
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Houston Fire Department officials don't yet know what sparked the flames. The building was closed and locked up at the time.
No injuries were reported.
The pastor told ABC13 that they had a food pantry scheduled for Saturday, but that will probably have to be rescheduled.
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"We're just going to get together as a group and decide which way we are going to go forward. We're still going to worship because church is not the building, church is the people," Pastor Michael Smith said. "So we'll just pray and seek God's guidance as we move forward."
ABC13 cameras captured parishioners gathered in the parking lot, holding hands and praying as firefighters worked to extinguish the flames.
The pastor said the church has been there nearly 76 years.