In the geological history of my planet, the plate tectonics resulted in the assembly of a kind of "ring supercontinent", that completely encircled a portion of the ocean and isolated it from the rest of the planet for a hundred million years or so.
It happened very shortly (geologically speaking) after the life on the planet discovered the joys of having vertebrae (Roughly analogous to the Silurian-Devonian or so in the Earth's history), and this configuration of continents lasted long enough that the species in the interior ocean and on the outside have been evolved separately, which had resulted in the rise of two distinctly different convergently evolved bony vertebrate lineages (Among the whole bunch of other parts of the biosphere), that have quite distinct anatomical structures that will in the future evolve into true bony skeletons, which in turn will result in the planet having two distinctly different types of land animals.
Sometime after that, the continents supposedly broke up and allowed the two biospheres to mix up. At the time of the continental break up the interior ocean had a surface area of about 3\5 of the Atlantic.
Is there a way for them to do that in such a way that they both biospheres survive this mixing up, without one lineage out-competing the other into oblivion?
Them coming out of mixing uneven is fine, my current worldbuilding states that descendant species from the inside of the continental circle consist only about 30% of all the vertebrates.
If you don't think so, please provide the next best thing that could result in drastically different skeletal structures of vertebrate animals (The kind I seek doesn't have a different amount of limbs or anything like that, but the shape of the bones and in particular the anatomy of the skull and jaws is entirely different to the point that I don't think that one could plausibly evolve out of the another, mostly the skull, since even 500 million years later, basically all vertebrate life on Earth still shares same general skull anatomy with those first 420 million-year-old jawed fishes, so I came to the conclusion that the point of divergence should be then or earlier).