Ft. Bliss SFC Crispen Hanson, 38, was arrested and charged with capital murder Monday.
An El Paso Police Department spokesman said the victim, 1-year-old Malachi Cosby, was Hanson's son.
Police said Cosby's body was found at his home on April 9 and detectives treated it as a suspicious death from the start. A grand jury reviewed the evidence late last week, and now Hanson is in jail on $700,000 bail.
A March 2012 Army publication describes Hanson as head coach of the Team Bliss Junior Olympic Track Club working directly with young children.
ABC-7's video archives show Hanson during a February 2010 vigil he led for his daughter Aiyana, who had died of leukemia. According to the archives, Hanson was then a single father with two other children.
Fort Bliss officials said Hanson is now married to Kintara Cosby, another soldier. Cosby's Facebook profile shows a picture of Malachi.
The indictment against Hanson shows one count of capital murder, one count of murder, and two counts of injury to a child stemming from incidents in August 2011 and September 2011 during which Hanson allegedly twisted Malachi's leg and hit it with an unknown object.