31-year-old Christopher Williams was arrested Monday at his residence on the 300 block of E 5th Street in Wilmington.
The arrest comes at the conclusion of a forensics investigation that began earlier this month, which indicated that the victims, ages 4 and 6, were assaulted by Williams over a period of time.
Authorities say the attacks happened while Williams was living with the mother of the victims at a home on 1200 block of Sycamore Street.
Williams is charged with three counts of second degree rape, four counts of sexual abuse of a child by a person of trust, second degree unlawful sexual contact.
He is currently jailed on $450,000 bail.