Stakes winner American Sailor and the unraced Beastie D were named as the two horses trained by Wayne Potts who perished in the blaze at Barn 60.
American Sailor, a nine-year-old gelding, was the winner of 15 races and over $568,000 (£411,000) in prize-money, who was awarded the G3 Troy Stakes on the disqualification of Imprimis on his most recent start at Saratoga last year.
A statement from the New York Racing Association said: "On Tuesday evening at approximately 6:05pm, the NYRA responded to an active fire affecting Barn 60 at Belmont Park. NYRA security was joined by backstretch staff in rendering immediate assistance to the horses stabled in the barn at the time of the incident.
"The fire was restricted to Barn 60 which holds stalls for horses under the care of trainers Wayne Potts and Jeffrey Englehart. A total of 58 horses were safely evacuated from the barn as a result of the immediate response by NYRA security, backstretch staff and the Elmont Fire Department.
"Despite the best efforts of those involved in the rescue, two horses under the care of Wayne Potts perished as a result of the fire. Those horses will be identified following appropriate notifications. There were no reported injuries to barn staff or NYRA employees."
The NYRA said that the local fire department responded within minutes to put out the fire and secure the scene. The New York State Fire Marshal and officials from Nassau County are investigating the cause,
Dave O'Rourke, NYRA President & CEO, praised the efforts of backstretch workers who rallied around to help with the rescue effort.
He said "The tragic loss of both horses will be deeply felt by the hard working women and men of the New York racing community, who dedicate themselves to the sport and to the care of these equine athletes.
"That collective dedication and sense of community was on display this evening, when the heroic and selfless response of so many prevented further loss and saved the lives of dozens of horses."