—We present results of study of the molecular composition of organic matter (OM) in the bottom sediments of the Laptev Sea by gas chromatography–mass spectrometry, isotope gas chromatography–mass spectrometry, and Rock-Eval pyrolytic analysis. The OM of all collected sediment samples shows a significant terrigenous contribution. Compounds that are biomarkers of methanotrophic microorganisms are also found. A positive correlation between the contents of the studied biomarkers and the contents of pelite and total organic carbon is observed at the sites with documented intense methane bubbling. For example, the average content of C30 hopenes at the “methane” stations is twice higher than that at the “background” ones. The average content of C32 αβ-hopanes in sediment samples from the methane seepage area is 1.5 times higher than that at the background stations. We suggest that the increased C30 αβ-hopane content (~1.5 times higher within the methane seepage area) and the decreased moretane index relative to the C31 hopane index are due to the inflow of OM of petroleum origin. The presence of biphenyl in sediments indicates its petroleum origin, which supports our assumption of the migratory nature of petroleum hydrocarbons in the methane seepage area. Triterpenoids found in the sediment OM indicate diagenetic bacterial transformation of OM in the methane seepage areas, which shows that methane has been released for a long time. We assume the intense activity of the consortium of methanotrophs and sulfate reducers in the methane seepage areas.