Xenophyophorea are giant deep‐sea rhizopodial protists of enigmatic origins. Although species were described as Foraminifera or sponges in the early literature, the xenophyophoreans are currently classified either as a class of Rhizopoda or an independent phylum. To establish the phylogenetic position of Xenophyophorea, we analysed the small subunit (SSU) rRNA gene sequence of Syringammina corbicula Richardson, a newly described xenophyophorean species from the Cape Verde Plateau. The SSUrDNA analyses showed that S. corbicula is closely related to Rhizammina algaeformis , a tubular deep‐sea foraminiferan. Both species branch within a group of monothalamous (single‐chambered) Foraminifera, which include also such agglutinated genera as Toxisarcon, Rhabdammina , and Saccammina , and the organic‐walled genera Gloiogullmia and Cylindrogullmia . Our results are congruent with observations of similar cytoplasmic organisation in Rhizammina and Syringammina . Thus, the Xenophyophorea appear to be a highly specialised group of deep‐sea Foraminifera.