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On the Pokemon status screen, underneath the Pokemon and to the left of the custom markings, is a small blue pentagon:
This doesn't seem to be present on Pokemon obtained through the Pokemon Transporter from Gen V:
I've looked into it myself, and popular opinion seems to be that it's either some kind of "Legitimate Pokemon" mark or simply to indicate that the Pokemon originates from Gen VI.
The latter seems far more likely to me, but do we know for sure what this blue hexagon means?
It's apparently a Kalos Region checker. Pokemon native to Kalos have it. It is not, as some say, a hack checker. This is easy to confirm since Pokemon Transporter straight-up won't import many hacked and some not hacked pokemon.
With the introduction of Pokemon Omega Ruby and Alpha Sapphire, the blue pentagon does not mean that the pokemon is native to Kalos, but it is a pokemon obtained in either XY or ORAS (6th generation). Thus, any pokemon except certain event pokemon can legally have a blue pentagon.
