Maristentor dinoferus was described in 2002, after it was first discovered on the coral reefs on Guam in 1996. However, until now its phylogenetic position has been puzzling. The 18S-ITS1-5.8S rDNA sequence of M. dinoferus is 320 by including 222 by from 18S rRNA gene, 77 by from ITS1 region and 22 by from 5.8S rRNA gene. Comparison of lengths of the ITS1 domain from the main ciliate groups (classes) was done, and it shows that short ITS1 may be the characteristics of heterotrichs. 18S rDNA sequence of M. dinoferus was analyzed using distance-matrix, maximum-parsimony and maximum-likelihood methods. In all three phylogeny trees M. dinoferus is clustered with heterotrichs and as a basal Glade within the heterotrich lineage, whilst not grouped with three Stentor species which were clustered with Climacostomum as a terminal Glade. This topology suggests that Maristentor is a holotrichous ciliate (the class Heterotrichea) and should not be placed in the family Stentoridae, but be given a new taxonomic position.