Bertin Salgado, 63, of Chicago is the minister at Iglesia Manantial de Vida on the South Side.
He's charged with aggravated criminal sexual abuse of two family members under 18.
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Prosecutors say the abuse of one of the girls happened at the church; they said the other took place at his home.
A sign at the church said Salgado is pastor.
The church did not immediately respond to a request for comment.
This is a developing story; check back with ABC7 Chicago for updates.