The Macintosh version of Linnaeus II now runs natively under Mac OS X 10.1 or higher but also under older versions of Mac OS (versions 8.6 and higher). The interface has been redesigned for Mac OS X and on both PC and Mac most windows are now resizable and can be maximized as well as minimized.

Text fields can now hold more than 32,000 characters on the Mac (text fields are still limited to 32,000 characters in the Windows version). The standard font in Linnaeus II has been changed to 11-point Verdana on the Mac and 8-point Verdana on the PC.

Linnaeus for Mac now supports more multimedia formats. In addition to PICT format images, you can now also use TIFF and JPEG format images. In fact, we highly recommend that you use TIFF and/or JPEG for all images, as this will simplify the process of porting your project from Macintosh to Windows (or vice versa). The PICT format is not supported in the Windows version.

Linnaeus II version 2.6 no longer has a Lower Taxa module; taxa below species level are now stored in the Species module. Taxa below species level now have a four-word name also indicating the subspecific rank, e.g., the subspecies 'Terrapene carolina mexicana' becomes 'Terrapene carolina subsp. mexicana'.

The Taxonomy field in the Species and Higher Taxa modules is now called the Classification field. The available taxonomic levels have also changed - the highest available level is now domain (in previous versions, the highest level was kingdom), while the number of available taxonomic levels below species level has been reduced to five: subspecies, variety, subvariety, form and subform. You can now enter you own kingdom and phylum names, while in previous versions you were restricted to a preset list of names taken from Margulis & Schwartz' Five Kingdoms.

The Index now allows you to list the epithets of species and lower taxa names as well, e.g. "exigua (Janthina)" for the species Janthina exigua. If you choose to include synonyms in the Index, epithets of the synonyms will also be listed in the Index. In addition, the Index module is now better at handling duplicates –– two or more taxa with the same synonym or common name.

In IdentifyIt, the Identify menu has been overhauled. File commands (e.g. 'Open Identify File', 'Save Identify File') have been moved to the File menu, while the commands Search Unknowns, Add Unknowns and Remove Unknowns have been replaced by a single command, Include Unknowns, which can be toggled on and off to indicate whether you want to take unknown (undefined) characters into account when calculating the match percentages. Another important interface change is the Add button under the Identify tab, which has been renamed Define and opens a window called Define Search Pattern.

The Find/Replace function now allows you to limit your search to one or more fields in a module, e.g. you can search the name field only, ignoring the other fields. To access this feature, choose Select Fields from the popup menu at the top of the Find window, marked 'Search in'. Another new feature is the Replace & Find button in the Replace window which lets you replace the currently selected hit and jump directly to the next hit.

The Run Demo feature (accessible from the File menu) now allows you to skip the fields during the demo and only show the pictures linked in the Multimedia field of the Species and Higher Taxa modules.

Find Hotwords now supports literature reference links in the format 'author (year)' as well. Verify Multimedia Files is a new command in the File menu that allows you to check whether all linked multimedia files can be found, verifying that none of the files have been accidentally renamed, deleted or moved to a location where Linnaeus II can't find them. Port Multimedia Files lets you generate a folder with cross-platform multimedia and identify files (i.e., files with names that are valid in both Macintosh OS and Windows).

The Picture Key of Linnaeus for Mac has a redesigned interface to match the Windows version. And new text-only choices now get a standard size, so you can easily use the Picture Key as a text key (with the occasional picture-based choice) as well.