Prosecutors say 41-year-old Carmella Martinez and 43-year-old Paul G. Martinez were arraigned Thursday on a 49-count indictment.
The Arroyo Seco residents are accused of conspiracy, theft from programs receiving federal funds and theft of government property.
The two entered not guilty pleas and were released pending trial under pretrial services supervision and other conditions.
The indictment alleges that between November 2003 and December 2011, Carmella and Paul Martinez stole federal funds provided by the U.S. Department of Housing and Urban Development for a Taos County program that provides affordable housing for low-income residents.
During that time, Carmella Martinez was a financial specialist for the TCHA and later its executive director.