Glycosphingolipids (GSLs) in membrane microdomains participate in important biological functions. In the present paper, we propose a novel model of the distribution of GSLs in membrane microdomains composed of sphingomyelin (SM) and cholesterol. We investigated the distribution of the ganglioside GM3 in a lipid membrane reconstituted with lipid extract from mouse B16 melanoma cells using an atomic force microscope (AFM). The surface topography of the reconstituted lipid bilayer showed three areas of different heights. The highest area was confirmed to be a GM3 domain by labeling with wheat germ agglutinin. To identify the lipids which are contributed to make the topography, the topographies of the artificial lipid bilayers composed of GM3, SM, 1-palmitoyl-2-oleoyl-phosphatidylcholine, and cholesterol were investigated. AFM images of the artificial lipid bilayers showed that the GM3 domain surrounded by a SM-containing phase only occurred, and its formation was found to depend on the cholesterol content.