Chautauqua County was established in February 1811 when the 1810 tax rolls verified a population of more than 500 taxable inhabitants. Mayville was selected as the county seat and the first courthouse was constructed between 1812 and 1815 (the War of 1812 slowed construction). The county, lake, and town of Chautauqua were all originally spelled with an ‘e' at the end, until 1859 when the county's Board of Supervisors voted to change the spelling to Chautauqua. The County originally had just two towns, Pomfret and Chautauque, and all other towns were taken from these as the population grew.
The last town to be formed in the county was North Harmony, taken from the town of Harmony in 1918.
The County Archives, located in the courthouse complex in Mayville, is the largest repository of historical documents in Chautauqua County. The archive includes many of the county's earliest legal and court records dating from 1811. Since 1997, the records management program has utilized grant funds to improve the storage and preservation of historical documents. The work is ongoing.