Some species, such as the aptly named T. spinalis, show a spine-like tube extending to the outside, which is not surrounded by the cortex.

The cortex of most species is either lamellar or consists of a web-like network, although in T. rauserae and the dubious T. tubularis it is micritic.

The interior structure is mostly tubular, regular, or irregular, with T. alcicornis and T. ramosus being unusual for their multi-branched chambers.

[2] Tubiphytes (and Nigriporellidae as a whole) has been identified as a number of different lineages, including sponges, red algae, cyanobacteria and hydrozoans.

Riding and Guo (1992) suggested that Tubiphytes is likely a sponge, due to the growth style and microfabric structure closely resembling them.