ION was initially developed as a freely available, web accessible component of a larger project, "TRITON" (the Taxonomy Resource and Index To Organism Names system) by BIOSIS, the then publishers of the Zoological Record ("ZR") and Biological Abstracts, in approximately 2000.

Its initially stated aim was to provide basic nomenclatural and hierarchy information, plus ZR volume occurrence counts (reflecting use in the literature) for animal names, to identify the taxonomic group to which an organism belongs, and to link to further information from ZR (or initially, other collaborating organization).

The Intellectual Property and Science division of Thomson Reuters was subsequently acquired by Clarivate Analytics who continue to make ION available (as at mid 2019).

In 2011, Nigel Robinson of Thomson Reuters described an in-progress upgrade of the database to include an additional >200,000 names from a digitised version of Sherborn's Index Animalium, extending the content of ION back to the commencement of official zoological nomenclature in 1758.

[3][4] As at 2019, the Index contained over 2 million newly published names from 1758 onwards (with a small gap around the period 1850-1864 corresponding to the difference between the end of coverage of Index Animalium and the commencement of the "Zoological Record"), out of a total complement of over 5 million name instances, each with an associated unique numeric identifier (ION LSID).