Police say their investigation began in February after multiple ponies were injured at New Castle County Carousel Park and Equestrian Center in Delaware.
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During one incident, police say a 17-year-old black and white mare was found to be injured and had difficulty breathing.
During a later date, a 20-year-old mare was found with a cord tied around its rear legs, police say.
Video captured the suspect wearing a dark jacket during some of the assaults, but police say they were unable to identify him.
Police say on April 20, a 31-year-old brown mare was found to be sexually assaulted. Due to clothing covering on the suspect's face, officers were still unable to identify him.
After enhancing the electronic surveillance equipment, police were able to make an arrest.
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Michael Riego, 31, was allegedly observed tying up the rear legs of a pony around midnight on May 21.
Upon arrival, police found Riego hiding in the corner of the stall and taken into custody.
Riego is being charged with two counts of bestiality and two counts of burglary.
The investigation is still ongoing and additional charges are anticipated.
All of the ponies were treated by an equine veterinarian and have resumed normal daily activities.