Aliphatic hydrocarbons (HCs) can be used as a fingerprint of a given seed oil. Only by characterization of aliphatic HCs could contamination by mineral oil in that seed oil be confirmed. During the isolation of squalene from soybean oil deodorizer distillate, a significant amount of unknown HCs, ca. 44 wt%, was obtained. These seemingly-easy-to-identify HCs turned out to be much more difficult to elucidate due to the presence of an irresolvable complex mixture (ICM). The objective of this study was to purify and identify the unknown ICM of aliphatic HCs from soybean oil deodorizer distillate. Purification of the ICM was successfully achieved by using modified Soxhlet extraction, followed by modified preparative column chromatography, and finally by classical preparative column chromatography. FT-IR, TLC, elemental analysis, GC/FID, NMR and GC-MS analyses were then performed on the purified HCs. The GC chromatogram detected the presence of ICM peaks comprising two major peaks and a number of minor peaks. Validation methods such as IR and NMR justified that the unknowns are saturated HCs. This work succeeded in tentatively identifying the two major peaks in the ICM as cycloalkane derivatives.