By 1850, Batavia was large enough to have its own government. They had a town meeting so the citizens of Batavia had their say on how Batavia should be run. They held an election and Meredith Mallory was chosen to represent Batavia at township meetings. Joel McKee was chosen to be town clerk and was tasked for the making of reports of business that Batavia handled and was also elected to be Justice of the Peace. Daniel Hyde was elected to decide on property taxes. Joseph Whipple was elected to provide for the poor and to be one of Batavia's 2 policemen. The other policeman selected was Salem Phillips. There were 8 men selected to take care of the roads.
One of the 1st laws passed was that animals had to be put in pens and kept off the roads. The settlers voted to have the village form a government in 1856. Instead of all going to a town meeting, 5 men were elected to represent the citizens and to take care of village business. They were named the Board of Trustees.
There were 1,800 people residing in Batavia. By 1891, they elected John H. Miller as their 1st mayor. The City of Batavia still has this form of government with the Mayor, Aldermen, City Clerk and Treasurer that are elected by the people.