Thousands of Categories

I keep reading on the forums that having lots of categories is silly.

So how would recommend setting up a hierarchal structure like classifying a species?

Kingdom: Animalia
Phylum: Chordata
Class: Mammalia
Order: Carnivora
Family: Ursidae
Genus: Ursus
Species:

You don’t want to do it with a hierarchal custom post type because wordpress would have to run the whole table before output.

Any suggestions?

thanks