[11][12][13] A 2013 molecular study using small subunit rDNA found Syringammina and Shinkaiya to form a monophyletic clade closely related to Rhizammina algaeformis.

This study also suggested that many individual genera are polyphyletic, with similar body shapes convergently evolving multiple times.

[16] However, cladistic analyses based on molecular data have suggested a high amount of homoplasy, and that the division between psamminids and stannomids is not well supported.

Many form delicate and elaborate agglutinated tests—shells often made of calcium carbonate (CaCO3) and other foreign mineral particles glued together with organic cements[17]—that range from a few millimetres to 20 centimetres across.

[16] Species of this group are morphologically variable, but the general structural pattern includes a test enclosing a branching system of organic tubules together with masses of waste material.

A number of unique terms are used to refer to anatomical aspects of the group: The protoplasm of xenophyophores contributes less than 1% of the total mass of the organism.

These growth phases were approximately synchronous between specimens, but it is unclear if this is biologically or developmentally controlled; some evidence suggests the synchrony may have been due to chance.

Most are epifaunal (living atop the seabed), but one species (Occultammina profunda), is known to be infaunal; it buries itself up to 6 centimetres (2.4 in) deep into the sediment.

[3][4][29] Xenophyophore densities are highest on soft sediments; however, they may still be found on rocky substrates including basalts, canyon walls, and manganese crusts.

[18] The diet and feeding ecology of xenophyophores was long the subject of speculation; the fragile tests and deepwater habitat of the group makes in vivo observation difficult.

[30] A 2021 study that utilised isotopic labeling to examine the question of xenophyophore feeding confirmed rapid uptake of both diatoms and dissolved organic matter in the form of glucose.

[39] Modern examples of Paleodictyon have been discovered; however, no evidence of tests, stercomares, grannelares, or xenophyophore DNA was found, and the trace may alternately represent a burrow or a glass sponge.

[41] Local population densities may be as high as 2,000 individuals per 100 square metres (1,100 sq ft), making them dominant organisms in some areas.

Xenophyophores have been found to be "ecosystem engineers", providing habitat and serving as traps for organic particles, increasing diversity in the surrounding area.

As they occur in all the world's oceans and in great numbers, xenophyophores could be indispensable agents in the process of sediment deposition and in maintaining biological diversity in benthic ecosystems.

Scientists in the submersible DSV Alvin at a depth of 3,088 metres at the Alaskan continental margin in the Gulf of Alaska collected a spatangoid urchin, Cystochinus loveni, about 5 cm diameter, which was wearing a cloak consisting of over 1,000 protists and other creatures, including 245 living xenophyophores, mainly Psammina species, each 3–6 mm.