We characterised benthic invertebrate community composition in 11 oligotrophic, alpine lakes. Nematodes were the most abundant benthic taxa in most lakes but community composition differed markedly. Several relationships between the invertebrate taxa were found but there was no strong evidence that competition or predation shaped the benthic community structure. Most lakes were dominated by a few nematode species with cosmopolitan distribution. Obligate and/or facultative parthenogenetic species were most abundant. With increasing species richness, the overall sex-ratio increased and the relative abundance of parthenogenetic species decreased.