The morphologically unique genus Gastrocirrhus has been considered a distinct but systematically uncertain euplotid due to the absence of both morphogenetic and molecular information. Based on the small subunit rRNA gene sequence, the phylogenetic position of Gastrocirrhus monilifer Ozaki & Yagui, 1942 was re-addressed using multiple algorithms (neighbor-joining, maximum parsimony, least-squares, and Bayesian inference methods). Results indicate that: (1) all phylogenetic trees using different methods are nearly identical in topology, placing G. monilifer closest to Euplotidium arenarium; (2) Gastrocirrhus and Euplotidium form a monophyletic group, namely the family Gastrocirrhidae, and appear to be intermediate taxa bridging the evolution of the Diophrys-Uronychia and Euplotes-complexes (i.e. Euplotes, Certesia, and Aspidisca); (3) the order Euplotida is a paraphyletic group composed of three deeply diverged clades (Euplotes-Certesia-Aspidisca-Gastrocirrhus-Euplotidium; Uronychia-Diophrys; and Prodiscocephalus); (4) together with Prodiscocephalus, the Diophrys-Uronychia complex forms a group at the suborder level and is placed at the root of the order Euplotida, and (5) results from molecular analyses conspicuously challenge the conclusions deduced from morphological as well as morphogenetical investigations-the characteristics traditionally used to define the euplotid taxa at the generic level and/or above may not be uniformly reliable.