ABSTRACT: The Gotland Deep is a temporary anoxic basin in the central Baltic Sea that is frequently subjected to inflow events which result in oxygenation of the deep water. We examined the protistan community structure in this environment several months after such an inflow event by analyzing small subunit ribosomal RNA (18S rRNA) sequences from samples collected in the oxic–anoxic transition zone (200 m) and in the sulfidic waters below (220 m). While ciliates and fungal phylotypes in the clone libraries decreased (40 to 14% and 25 to 8%, respectively) from the transition zone to the deeper sulfidic waters, jakobid phylotype abundance increased from 7 to 32%. Heterotrophic choanoflagellates and stramenopiles accounted for 7 to 10% of the phylotypes at both depths. Other taxonomic groups (e.g. dinoflagellates, cercozoans, perkinsozoans, amoebae, centroheliozoans) were rare. Seven phylotypes were shared between the 2 libraries, with a higher number of phylotypes with broader taxonomic representation occurring in the sulfidic compared to the suboxic water sample. Only a small proportion (9%) of the 18S cDNA sequences in the Gotland Deep clone libraries were closely (>95% sequences similarity) related to previously described sequences.