The diversity of heterotrophic flagellates was examined at marine sediments around Cape Tribulation, Australia. The species described belong to the Alveolates, Apusomonadiae, Cercomonadida, Choanoflagellida, Cryptomonadida, Diplomonadida, Euglenozoa incertae sedis, Kathablepharidae, Kinetoplastida, Pedinellids, Stephanopogonidae, Stramenopiles, Stramenopiles incertae sedis, Thaumatomonadidae and Protista incertae sedis. Among the 51 species from 38 genera encountered in this study is one new taxon: Glissandra similis n. sp., and two new names are introduced: Goniomonas abrupta (Skvortzov 1924) nomen nodum and Cercomonas skvortzovi (Skvortzov 1977) nomen nodum. There was little evidence for endemism because most flagellates including one new taxon described here have been reported.