Rodney Sanders has been charged with two counts of murder.
His arrest came after the bodies of Sister Margaret Held and Sister Paula Merrill(pictured), both 68, were found at home on Thursday after they failed to arrive for work at a health clinic.
Speaking of his arrest, Lt Colonel Jimmy Jordan said: "Sanders was developed as a person of interest early on in the investigation."
It is understood the man is being held in an undisclosed detention centre awaiting an initial court appearance.
Tributes have been paid to the nuns who've served the Church for over 30 years. A celebration of their lives will take place on Sunday at St Thomas Church in Lexington where they had run Bible studies.
Diocesan chancellor Mary Woodward said the service would be "an opportunity for the diocesan community and friends to celebrate the lives of these two remarkable women".
Rev Greg Plata of St Thomas is calling on people pray for the killer or killers.
He said: "Forgiveness is at the heart of being a Christian.
"Look at Jesus on the cross: 'Father, forgive them for they know not what they do.'"
A motive for their killings is unknown but their stolen car was found abandoned a mile away from their home.