Mass spectrometry, especially coupled with gas chromatography or tandem, is the analytical method of choice in elucidation of biomarker compounds present in organic mixtures extracted from geological, environmental, or biological samples. This review describes the biomarker concept; i.e., the precursor natural products to the geological/environmental derivatives, and their application as tracers in the geosphere and ambient environment. The mass spectrometric methods currently utilized for such analyses are reviewed, and typical examples of applications are described with a general key to the literature.