Trace fossils are generally difficult or impossible to assign to a specific maker. Only in very rare occasions are the makers found in association with their tracks. Further, entirely different organisms may produce identical tracks. Therefore, conventional taxonomy is not applicable, and a comprehensive form of taxonomy has been erected. At the highest level of the classification, five behavioral modes are recognized:
* Domichnia, dwelling structures reflecting the life position of the organism that created it.
* Fodinichnia, three-dimensional structures left by animals which eat their way through sediment, such as deposit feeders;
* Pascichnia, feeding traces left by grazers on the surface of a soft sediment or a mineral substrate;
* Cubichnia, resting traces, in the form of an impression left by an organism on a soft sediment;
* Repichnia, surface traces of creeping and crawling.
Fossils are further classified into form genera, a few of which are even subdivided to a "species" level. Classification is based on shape, form, and implied behavioural mode.
To keep body and trace fossils nomenclatorially separate, ichnospecies are erected for trace fossils. Ichnotaxa are classified somewhat differently in zoological nomenclature than taxa based on body fossils (see trace fossil classification for more information). Examples include:
*Late Cambrian trace fossils from intertidal settings include Protichnites and Climactichnites, amongst others
*Mesozoic dinosaur footprints including ichnogenera such as Grallator, Atreipus, and Anomoepus
*Triassic to Recent termite mounds, which can encompass several square kilometers of sediment