The complete small subunit rRNA gene sequences of two scuticociliates, Paranophrys magna Borror, 1972 and Mesanophrys carcini Grolière & Leglise, 1977, were determined. The results show that each comprises 1759 nucleotides. The phylogenetic positions of both species within the subclass Scuticociliatia were deduced using distance matrix and maximum parsimony methods. The trees indicate that the order Philasterida is probably a monophyletic group, within which Mesanophrys carcini is allied in a clade with Anophryoides haemophila that branches basally to other four species: Paranophrys magna, Uronema marinum, Pseudocohnilembus marinus and Cohnilembus verminus, while the clade including Paranophrys magna and Uronema marinum is grouped with that of Pseudocohnilembus marinus and Cohnilembus verminus.
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