Triterpenoids and fatty alcohols were identified from the sediments of five mangrove ecosystems (Kunjimangalam, Pazhayangadi, Pappinissery, Thalassery, and Kadalundi) in the northern Kerala coast, India, to illustrate the organic matter sources. Straight chain fatty alcohols in the range C12–32 were detected, and among these the long chain fatty alcohols (C20–32) were exclusively even chained compounds. Branched fatty alcohols (6,10,14-trimethyl-pentadecan-2-ol and 3,7,11,15-tetramethyl-2-hexadecanol) of bacterial origin were detected in a few observations. Twenty triterpenoids were detected from the study region in which 13 of them were sterols. Triterpenoids originated from higher plants such as stigmasterol, campesterol, β-sitosterol, taraxerol, lupeol, germanicol, β-amyrin, α-amyrin, and betulin were identified in the study. Brassicasterol, a diatom marker and dinosterol, a dinoflagellates marker were also detected in the study region. An elevated % composition of dinosterol and dissolved oxygen super-saturation were noticed in Kunjimangalam during pre-monsoon, which may suggest elevated input of algal organic matter in the mangrove system. Cholesterol transformation products such as coprostanol and epi-coprostanol were detected, which indicated the presence of fecal contamination in the sedimentary organic matter. From the ternary diagram, it was recognized that the organic matter contribution from marine algae was feeble as compared to terrestrial input.