Over the last few decades, the occurrence of long chain alkenones (LCAs) in Quaternary lacustrine settings has been reported, the distributions being remarkably different from those of open ocean settings. We report here the occurrence of LCAs with modern lake-type composition from Middle Miocene sedimentary strata in the Dahonggou Section, Qaidam Basin, northern Tibetan Plateau. This is the first report of LCAs with preserved lake compositions in pre-Quaternary lacustrine sediments. The discovery implies that the producers of modern lacustrine LCAs could originate from similar lake species living at least as far back as the Miocene epoch. It also sheds new light on the potential of “alkenones” as palaeotemperature indicators in lacustrine systems back to at least 10.5 Ma.