Margel Tenney was arraigned Wednesday in Lewis County on two counts of sexual abuse by a parent or guardian.
State Police say Tenney is accused of sexually abusing two family members, who are both 14-years-old.
Investigators have been looking for Tenney since Tuesday night when an Amber Alert was issued for Shaina Nicole Tenney, 16, and her seven-month-old daughter, Grace.
Investigators believed both girls were in "extreme danger" at the time the alert was issued.
Police say Margel Tenney is Shaina Tenney's stepfather.
Troopers say they are not sure why Tenney took the girls, but they are not the victims in the abuse case.
Troopers say the girls were not hurt and Tenney was arrested without incident. The two girls are now in the custody of Child Protective Services.