Federal prosecutors say Ziming Shen and Joanna Fan, of Staten Island, diverted money from a chain of preschools they owned to their private business interests, and also to make mortgage payments on several condominiums.
They were arraigned before a federal magistrate in Brooklyn on Friday, and released after each posted $750,000 bail.
Their lawyer, Barry Agulnick, told reporters the couple would defend themselves vigorously.
The couple operate the Red Apple Child Development Center, which has six schools across the city.
After his court appearance, Shen was arrested again when kicked at news photographers outside the courthouse.