The abundance, diversity, taxonomic composition and functional structure of benthic ciliate assemblages were studied in the intertidal zone of two estuaries with contrasting conditions. The Chernaya (CH) is a small (2-km long) sub-Arctic estuary in the White Sea; the Vellar (VE) is a large (20-km long) tropical estuary in the Bay of Bengal. At both sites, the average abundance and biomass of ciliates were similar and quite typical of other marine interstitial habitats. The diversity was high (114 species in CH; 39 taxa, mainly identified to the genus or putative species level, in VE). Spatial distribution patterns in abundance, biomass and taxonomy-based diversity indices differed between the estuaries. In contrast, most functional traits followed similar trends in both estuaries. In particular, from the riverine part seaward, the ratio of raptorial algivorous ciliates to bacterio- and detritovore fine filter feeders increased, as well as the ratio of crawling or gliding ciliates to free-swimmers. Mean body size and oblongness also increased seaward. No clearly defined diversity minima were found in the mid-estuary oligohaline zones. The results are discussed in the context of some general concepts in estuarine ecology.