The diversity and mode of life of microbial eukaryotes in hydrothermal systems is very poorly known. We carried out a molecular survey based on 18S ribosomal RNA genes of eukaryotes present in different hydrothermal niches at the Mid-Atlantic Ridge. These included metal-rich and rare-earth-element-rich hydrothermal sediments of the Rainbow site, fluid-seawater mixing regions, and colonization devices (microcolonizers) containing organic, ironrich, and porous mineral substrates that were exposed for 15 days to a fluid source. We identified considerable phylogenetic diversity, both at kingdom level and within kinetoplastids and alveolates. None of our sequences affiliates to photosynthesizing lineages, suggesting that we are targeting only autochthonous deep-sea communities. Although sediment harbored most phylogenetic diversity, microcolonizers predominantly contained bodonids and ciliates, indicating that these protists pioneer the colonization process. Given the large variety of divergent lineages detected within the alveolates in deep-sea plankton, hydrothermal sediments, and vents, alveolates seem to dominate the deep ocean in terms of diversity. Compared with data from the Pacific Guaymas basin, some protist lineages seem ubiquitous in hydrothermal areas, whereas others, notably kinetoplastid lineages, very abundant and diverse in our samples, so far have been detected only in Atlantic systems. Unexpectedly, although alvinellid polychaetes are considered endemic of Pacific vents, we detected alvinellidrelated sequences at the fluid-seawater interface and in microcolonizers. This finding can boost further studies on deep-sea vent animal biology and biogeography.C ompared with prokaryotes, microbial eukaryotes thriving in extreme environments have rarely been studied. This fact is partly because of the difficulties imposed by classical cultivation approaches. Recent eukaryotic diversity surveys based on 18S rRNA are revealing an unexpected variety of often divergent lineages in different biotopes, including some extreme environments (1-6). The only available molecular survey of microbial eukaryotes from deep-sea vents was recently carried out in hydrothermal sediments from the Pacific Guaymas basin and revealed an important diversity of hitherto unknown lineages (5). Surprisingly, many of these sequences affiliated to typical photosynthesizing groups (such as green algae or diatoms), leading to the conclusion that autochthonous eukaryotes cannot be distinguished from those deposited from the water column (5). There were two objectives in this study. First, we aimed at characterizing the diversity of autochthonous microbial eukaryotes from Mid-Atlantic Ridge hydrothermal systems. Thus, we have carried out a molecular survey of hydrothermal sediment and seawater-fluid interface. These results should constitute a first base for comparison with data from the Pacific systems. To date, whereas prokaryotes seem ubiquitous in different oceanic regions (7), possibly including vent areas, metazoans are subject to a defi...