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Saratoga NFH, established in 1911, has served as an egg-producing station during most of its years of operation. Between 1915 and 1984, various strains of brook, rainbow, brown, golden and cutthroat trout and Dolly Varden eggs were produced. In 1966, Saratoga NFH was formally designated as a broodstock hatchery, and in 1984 the hatchery became involved in the Great Lakes lake trout recovery program. Today, the hatchery's broodstock program includes supplying about 5 million eyed Lewis Lake lake trout eggs to the Great Lakes restoration program and 3 to 4 million Plymouth Rock brown trout eggs for Service, State, and Tribal hatcheries nationwide.
In 1997, Saratoga NFH adopted a unique role in becoming the first hatchery in the NFHS to become involved in rearing endangered amphibians. The Wyoming toad, found only in southwestern Wyoming, is considered the most endangered amphibian in North America. The hatchery maintains a captive population for breeding, rearing, and refugiá, and progeny from this program will be used for reintroduction efforts.