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Despite the planktonic ciliate importance in the microzooplankton compartment, their full-depth vertical distribution in the Arctic Ocean was poorly documented as well as the related variations in different water masses. The full-depth community structure of planktonic ciliates was investigated in the Arctic Ocean during summer 2021. The ciliate abundance and biomass decreased rapidly from 200 m to bottom. Five water masses were identified throughout the water column and each one exhibited a unique ciliate community structure. Aloricate ciliates were singled out as the dominant group with average abundance proportion to total ciliates at each depth >95%. Large (>30 μm) and small (10–20 μm) size-fractions of aloricate ciliates were abundant in shallow and deep waters, respectively, which revealed an anti-phase relationship in vertical distribution. Three new record tintinnid species were found during this survey. Pacific-origin species Salpingella sp.1 and Arctic endemic species Ptychocylis urnula occupied the top abundance proportion in the Pacific Summer Water (44.7%) and three water masses (≥38.7%, Mixed Layer Water, Remnant Winter Water, Atlantic-origin Water), respectively. The habitat suitability of tintinnid abundant species was characterised by the Bio-index revealing a distinct death-zone for each species. Variations in survival habitat of abundant tintinnids can be regarded as indicators for the future Arctic climate change. These results provide fundamental data on the microzooplankton response to the intrusion of Pacific waters into the Arctic Ocean upon its rapid warming. [Display omitted] • Full-depth vertical distribution of ciliates was analysed in the Arctic Ocean. • Aloricate ciliates were more abundant than tintinnids. • Each water mass had unique ciliate community structure. • A novel bio-index for tintinnid survival habitat can be regarded as indicator for Arctic Warming. [ABSTRACT FROM AUTHOR]