Efficient separation and accurate quantification of sphingolipids (SL) are important for studying SL concentrations and biological functions. The objectives of this study were to develop effective methods for the separation and quantification of SL and to determine the relationship between palmitate and SL contents of mature soybean seeds. Methods using column chromatography and high-performance liquid chromatography−evaporative light scattering detector (HPLC-ELSD) were developed to separate and quantify glucosylceramide (GlcCer) and ceramide (Cer) in 15 soybeans lines in which palmitate content ranged from 3.7 to 40.7%. There were significant differences among the lines for GlcCer (83.4−397.6 nmol/g) and major Cer contents (8.4−20.7 nmol/g) on a dry weight basis. The correlations of palmitate content with GlcCer and Cer concentrations were not significant. The results indicated that the palmitate content of soybean seed did not affect their GlcCer and Cer contents. Genetic factors other than those that control palmitate content seemed to be responsible for the variation among soybean lines for GlcCer and Cer contents.