Vertically, I suppose. I'm not a biologist. I use the term as a layman would.
BTW, that would be two of every biblical kind, not two of every species...the two should not be confused.
But if two of every biblical kind were on the Ark, then wouldn't speciation have had to occur over the subsequent 4000+ years?
If you count generations, you have to do so both vertically and horizontally within each kind and subkind/species. When you do this, it doesn’t take very long to hit millions of generations. And yes, speciation of land animals would have to have occured in the last 4500 years or so. For more on rapid speciation, you might want to give the following a read:
http://www.icr.org/article/4559/