Biphytanes, which are derived from glycerol dialkyl glycerol tetraether (GDGT) lipids, are biomarkers for the presence of Archaea in geological samples. They (especially cyclic structures) are rarely reported from sediments or oils that are older than the Triassic period, where their first record may be traced back to the Late Archean. There have been only two studies that have reported diagenetic products of cyclic biphytanes using two dimensional gas chromatography. In this study, we used full scan and multiple reaction monitoring (MRM) mass spectrometry (MS) to tentatively assign a series of diagenetic products of cyclic biphytanes within uppermost Permian and Lower Triassic sedimentary rocks. We observed three distinct groups derived from mono-, bi-, or tricyclic biphytanes, echoing previous studies. Each group could be further divided into three discrete series according to structure and composition. Using MRM also revealed that numerous sedimentary rocks contained such diagenetic products, but at trace concentration below the limit of detection of full scan MS. This indicates that the presence of Archaea-containing GDGT lipids has been underestimated within paleoenvironments. Episodic occurrences of biphytanes in the Permian-Triassic transition also provide additional evidence for the distribution of Archaea in the geological past.