The first position of San Miguelito, was known by the names of villages and settled east of the current location, which was founded by rubber tappers and raicilleros between 1.850 and 1.855. In the last century San Miguelito, was of great commercial importance, this activity was carried through the railway project which covered the route from this town to Punta Mico, in the Atlantic Ocean to build on the extraction of rubber and rootlet that abounded in the area.

Currently the town occupies the lower and western hill of the old seat, on the eastern shore of Lake Nicaragua.