Sub-diffraction optical imaging with nanometer resolution of lipid phase separated regions is reported. Merocyanine 540, a probe whose fluorescence is sensitive to the lipid phase, is combined with super-resolution imaging to distinguish the liquid and gel phase nanoscale domains of lipid bilayers supported on glass. The monomer-dimer equilibrium of MC 540 in membranes is deemed responsible for the population difference of single molecule fluorescence bursts in the different phase regions. The extension of this method to other binary or ternary lipid models or natural systems provides a promising new super-resolution strategy.