The Mangshan pit viper, Protobothrops mangshanensis, is a rare, highly endangered snake native to the mountainous regions of Hunan Province in China. Snakes possess abdominal scent glands, which have been chemically studied in several species. These glands can contain various lipids and peptides, but very often also complex mixtures of carboxylic acids. We report here the occurrence of novel methyl-branched unsaturated acids found in the secretions of six captive individuals living in a zoo. The structures of these compounds, 4.6-dimethylalk-5-enoates in a homologous series from C11–C16, were characterized by GC–MS and GC–IR analysis and various microderivatization reactions including hydrogenation and esterification leading to methyl and pyridylmethyl esters. In addition, dimethyloxazoline formation helped to localize the double bond. The synthesis of methyl 4,6-dimethyldodec-5-enoate allowed the correct assignment of structures and showed the (E)-configuration of the double bond for the major naturally occurring diastereomers. These acids occur in small amounts compared to the major glandular components, cholesterol, and 1-O-hexadecylglycerol, as well as other common long-chain alcohols and amides. Although a general defensive function has been proposed for snake abdominal scent glands, the specific chemistry and moderate amounts of acids reported here may suggest a function in chemical signaling for the Mangshan pit viper. In addition, proline-containing diketopiperazines were identified for the first time in snake scent glands, although an artificial formation from amino acids likely present in the secretion cannot be excluded.