Lake Cadagno (26 ha) is a crenogenic meromictic lake located in the Swiss Alps at 1921 m asl with a maximum depth of 21 m. The presence of crystalline rocks and a dolomite vein rich in gypsum in the catchment area makes the lake a typical “sulphuretum ” dominated by coupled carbon and sulphur cycles. The chemocline lies at about 12 m depth, stabilized by density differences of salt-rich water supplied by sub-aquatic springs to the monimolimnion and of electrolyte-poor surface water feeding the mixolimnion. Steep sulphide and light gradients in the chemocline support the growth of a large bacterial plume (up to 107 cells ml−1) dominated by green sulphur bacteria (GSB) of the genus Chlorobium and purple sulphur bacteria (PSB) of the Chromatiaceae family. Since the early Holocene (10.5–8 cal kyr BP), PSB and GSB are showing long-term alternation in abundance and relative dominance. Key species are Chlorobium clathratiforme , Thiocystis chemoclinalis , Thiocystis cadagnonensis , Candidatus “ Thiodictyon syntrophicum ” and Chromatium okenii ; the latter represents only 0.3 % of the total cell number but due to its big size and high activity can contribute up to 70 % of the total carbon uptake in the chemocline. Small-celled PSB together with the sulfate-reducing bacterium Desulfocapsa thiozymogenes sp. form stable aggregates in the lake, which represent small microenvironments with an internal sulphur cycle. Eukaryotic primary producers in the anoxic zones are dominated by Cryptomonas phaseolus , whereas eukaryotic heterotrophs are represented by ciliates and choanoflagellates, but a clade of heteroloboseans and two novel clades distantly related to opisthokonts and Cercozoa are also present. Zooplankton and fish abundance in the mixolimnion of this model ecosystem are linked via food web to the chemocline microbial plume, consequently anaerobic primary production supports relative high fish productivity in the lake.