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Or vice versa. What reasons are there for choose one over the other?

hierarchical taxonomies

vs

multiple custom taxonomies

I realize the examples I gave may not be the best dummy data, but pretend, in this instance, that I have a blog for animal pictures. A single post could have both dogs and cats.

Performance? Issues trying to use Prev and Next links? URL structure? Or would both options be practically the same?

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If you needed an archive page that listed all dogs, then the hierarchical approach would be much efficient. You could visit `/category/dogs', and Bob's your uncle.

If you used separate categories for every breed of dog, then that dogs archive would require a custom query to select everything from every individual breed in the dogs taxonomy.

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