Rural crime investigators began an appeal earlier this month to find Achilles, an eight-year-old Clydesdale stallion last seen at his Putty Valley Road property about 8am on October 1.
Police described the bay horse as having a distinctive white splash over his right eye, a black mane and a white baldy face.
Last week Hunter Valley and Hawkesbury police searched another Putty property where they dug up a horse they will allege to be Achilles. A veterinary examination led police to allege "that the death was ultimately caused by a gunshot wound to the neck".
The property's 36-year-old owner was issued a court attendance notice for kill stock with intent to steal, commit an act of aggravated cruelty upon an animal and several firearm offences.
He will face Singleton Local Court on December 3.