Reaching to over 4000 m in altitude, the Bale mountains of south-central Ethiopia comprise the most extensive area of Afro-alpine and sub-alpine Ericaceous vegetation in Africa and host an exceptionally high number of endemic species. Previous pollen analyses of a sediment core of the glacial lake Garba Guracha, located at 3950 m altitude, indicate shifts of the Ericaceous and the Afroalpine belt in relation to climatic changes during the Holocene and imply that the ecosystem has been shaped by natural expansion and contraction of vegetation zones (Umer et al. 2007). At the same time, the significance and timing of the onset of anthropogenic impact, e.g. through grazing and through cutting and burning of Erica scrub, is debated. From Lake Garba Guracha we have retrieved sedimentary ancient DNA targeting the last 4000 years and focussing on plants and diatoms. Positive results were retrieved from nearly all samples. The vegetation revealed by the DNA is characterized by Afro-alpine species in all but the lowest sample, which shows a high number of reads assigned to Erica arborea - absent in the younger samples with ages less than 4000 yrs BP. This supports the previously postulated timing of the contraction of the Ericaceous zone, while, in contrast to pollen, it provides a local picture of the vegetation and reveals a high diversity in herbs and forbs, including endemic taxa. Diatom taxa identified by DNA experience a distinct turnover during the time period analysed, and, together with the aquatic plants, can elucidate lake ecosystem history. Interestingly, sequence data of plants was more consistent between PCR replicates than that of diatoms. Consistency in the plant data between replicates was high to an age of about 2500 yrs BP, while for diatoms, degradation as deduced from rates of success and reproducibility was not as clearly linked to depth. Thus, despite signals of DNA degradation, the results clearly demonstrate that authentic and informative DNA data can be retrieved over millenial timescales from Afro-alpine sites.