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- Your Ad Here Seneca County is a county located in the U.S. state of New York. As of the 2000 census, the population was 33,342. Two villages share the duty as the county seats: Ovid and Waterloo. History Seneca County was formed in 1804. Seneca County is the only county in New York to officially have two county seats. The name is from the Iroquois (Seneca) that occupied part of the region. ![]() |