Dylann Roof had a handwritten note detailing the names and addresses of several ethnic minority churches in the back of his car, police officer Brittany Burke said.
The agent was giving evidence in the second week of Roof's trial. The 22-year-old is accused of opening fire during a Bible study at the Emanuel African Methodist Episcopal Church in Charleston in June 2015.
Roof's defence has indicated it will offer no evidence and is unlikely to cross examine witnesses. Last week his lawyer David Bruck said the shooting "clearly did occur".
The jury heard on Tuesday how Roof was arrested after his car was stopped by police days after the shooting.
Officer Burke claimed that a alongside the list of churches was the name and of Denmark Vesey, one of the founders of Charleston's Emanuel AME Church.
He was a well-known campaigner against the slave trade and led a failed revolution in 1822. He was hanged and the church was burned down.
If he is found guilty Roof will go on to face a separate hearing on his fate. The prosecution is recommending the jury sentence him to death.
