In recent years,ancient DNA-basedmicrobial communities were retrieved from marine sedimentaryrecords, which were successfully applied to reconstruct local paleo-environmental changes. However, it is poorly known whether ancient DNA-basedmicrobial studies could be possible for reconstructing historic limnic environmental conditionsin lacustrine sedimentary records. Here,we investigatedthe diversity and abundance of light-dependent dinoflagellate algaein a 5.8 m sediment core(spanning the last 18,500 years) of Qinghai Lake using an integrated approach including polymerase chain reaction (PCR),denaturing gradient gel electrophoresis (DGGE),and quantitative PCR (qPCR). Our phylogenetic results showed that the dinoflagellate 18S rRNA gene sequences from this study were closely (~ 98% identity) related to marine algalspeciesWoloszynskiahalophila and Scrippsiellahangoei. qPCR results showed that the dinoflagellateabundance in the sedimentsalong the Qinghai Lake core was 2.27 * 10~3 ~ 8.55 * 10~6 copies per gram sediment,which wassignificantly (R = 0.408,p = 0.0001) correlated withtotal organic carbon(TOC) content. Parallel analyses revealed that lowdin of lagellate 18S rRNA gene abundance corresponded to low TOC and high conductivities of soluble salt,whereas high dinoflagellate gene abundance corresponded to high TOC and low conductivities of soluble salt. In the Qinghai Lake region,TOC can be served asan indicator of paleo-precipitation,which is related to historic nutrient input; while the conductivities of soluble salt indicated salinity fluctuation. Therefore,our data suggested that temporal variation of dinoflagellate 18S rRNA gene abundance preserved inthe Qinghai Lake sediments mightreflect the variations innutrient level and salinity sincethe latePleistocene in the Qinghai Lake region.