The Harris County Sheriff's Office said kidnapping charges have been filed against 25-year-old Jason Vasquez, who is believed to be the boy's uncle.
Police arrested and charged another man, 21-year-old Joel Vasquez, with interference with child custody, according to court documents.
Joel Vasquez's relationship with Jason Vasquez and the child remains unclear.
On Saturday, a regional Amber Alert notified Houstonian's phones that the child had gone missing after being last seen in the 15000 block of Green Stone Drive at around 3:15 p.m.
The sheriff's office said on Monday the boy was found safe, and a manhunt continues for Jason Vasquez.
Anyone with information Jason Vasquez's whereabouts are urged to call the HCSO Missing Person unit at 713-755-7427 or Investigator Benavides at 832-262-5238 or Investigator Quintanilla at 713-262-5193.