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Zelkova abelicea is an endemic tree growing only on eight mountain stands on the Greek island of Crete. The aim of this study was to determine the structure of the assemblages and analyze the diversity of the arachnid assemblages living on Zelkova abelicea, an endemic tree species in Crete. Material for the analyses was collected from tree trunks, oftentimes covered by bryophytes or lichens. In the examined material, 85 taxa were recorded. The most numerous groups represented in the analyzed material were Acari, including representatives of the orders Mesostigmata (78 ind. of 18 spp.) and Oribatida (1056 ind. of 51 spp.). In the order Mesostigmata the species represented by the highest numbers of specimens were Onchodellus karawaiewi (15 individuals) and Hypoaspisella sp. (13), which is probably a species new to science. In turn, representatives of the order Oribatida were much more numerous, with Zygoribatula exilis (284) and Eremaeus tuberosus (210) being identified in the largest numbers. Among the eight sampled localities, Gerakari (646 ind. and 50 spp.) and Omalos (409 ind. and 43 spp., respectively) had by far the richest assemblages. Statistical analyses confirmed the highly diverse character of the arachnid assemblages at the individual sites, which is a consequence not only of the varied numbers of arachnids found, but also of the presence of very rare species, such as Androlaelaps shealsi, Cosmolaelaps lutegiensis or Hoploseius oblongus. These results highlight the high species diversity of the arachnids found on Z. abelicea but also suggest the lack of connectivity between the isolated and fragmented forest stands on Crete.