The lightning struck the building around 9:40 p.m. on Wednesday.
Sea Turtle Recovery employees (STR) rushed to the hospital, and said, when they arrived, the West Orange, New Jersey Fire Department and others were working to put out the fire.
Sea turtles were exposed to heavy smoke, so they were moved to a safe building inside the zoo.
Staff and volunteers, along with zoo staff, immediately assessed the turtles.
Sea Turtle Recovery said that a critically endangered Kemp's ridley turtle, named Pickles, was in the hospital fighting a respiratory infection.
During his emergency exam, his heart rate dropped dangerously low.
Dr. Paluch, STR's vet, had the staff put Pickles in an emergency pool, which helped stimulate deeper breathing and helped him recover.
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"Our loggerhead, a green sea turtle, and all three Kemp's were stabilized. We headed the four hours to New York, as the Atlantic Marine Conservation Society began preparing their tanks for our arrival. Our day has not stopped, and we have been up without rest. The turtles are now safe, and they are being monitored closely," the recovery service said.
The organization is grateful to the fire department for putting out the fire and the staff who quickly spotted the blaze and got the animals to safety.
STR said that their tanks and filtration may have been damaged in the fire, but they have not been able to assess the equipment yet.
Visit seaturtlerecovery.org or text "SEATURTLE" to 202-858-1233 for more information on the turtles.
The Turtle Back Zoo was able to open on Thursday for normal hours.