The advisory includes northern Erie, Niagara, Orleans and Genesee counties.
It runs from 10 p.m. until 9 a.m. Tuesday, the weather service said.
Temperatures in those areas are forecast to dip into the mid 30s. Tender vegetation could be susceptible, forecasters said.
Meanwhile, in the freeze warning areas, forecasters say the thermometer could dip down to 30 degrees.
In Erie County, affected areas are expected to be in the southeastern part of the county away from the lake.
The forecast could prove particularly devastating for area farmers who are already under stress from several weeks of heavy rain following an unusually warm month of April.