• the taxonomic databases
• the supporting databases
• the identification tools
• the biogeographical information system

The taxonomic databases consist of two modules: Species and Higher Taxa. The Species module contains text and multimedia information on species within your taxonomic group: descriptions, synonyms, common (vernacular) names, taxonomic information, literature references, photographs, drawings, audio, video, etc. The Species module also holds information on subspecies and other taxa below species level. The Higher Taxa module can be used to store information on taxa above species level.

The supporting databases can be used to store additional information. The Navigator acts as the central point or "main menu" of your project; it can be used to navigate around Linnaeus II, and also stores information on scientists, students, publishers, and other contributors. The Introduction contains general and introductory material on the taxonomic group. The Glossary holds definitions for technical terms used in the program. The Literature module contains literature references. And the Index lists all described species and other taxa in alphabetical order, as well as (sub)species epithets, scientific synonyms and common (vernacular) names given for the described taxa.

There are three identification modules which let you identify a specimen based on its characters. The identification tool which will probably be most familiar to you is the Text Key™, because it simply is an electronic version of written dichotomous keys. The Picture Key™ is similar to the Text Key but is picture- rather than text-based, and therefore better suited to visual identification.

The third, most powerful identification tool is called IdentifyIt™. It is a multiple-entry key based on a matrix of taxa, characters, and character states. Unlike the Species and Higher Taxa, which hold text descriptions of the taxa, in IdentifyIt taxa are described in a more structured format: as a series of character states. This allows you to easily obtain answers to specific questions like, "Which species are red and/or white with wings and large feet?"

Linnaeus also contains a biogeographical information system called MapIt™. This grid-based system allows you to enter geographical data on species and other taxa, such as distributions and type localities. The data can then be used to, among other things, search for species occurring in a particular geographic region, compare the distribution of a species to that of another, or display species richness.