Not Rayquaza as an answer please or Primal kyogre. Both of them actually suck against Primal Groudon.
252 Atk Choice Band Rayquaza Earthquake vs. 252 HP / 56+ Def Primal Groudon: 212-250 (52.4 - 61.8%) -- guaranteed 2HKO
252+ SpA Primal Kyogre Origin Pulse vs. 252 HP / 200 SpD Primal Groudon in Heavy Rain: 1348-1588 (333.6 - 393%) -- guaranteed OHKO
To be honest Primal Groudon is the best Pokemon in the game right now, however has a few counters which topple it sideways.
Lugia laughs at Earthquake and can stall it out with Roost, Toxic and Ice Beam. Multiscale seals the deal.
Mega Salamence joins in with the Ground laughter and also has good physical bulk so it can set up and KO Groudon. Also Intimidate renders Groudon less useful.
Ground Arceus Is not used often, but Judgement or Earthquake will send Groudon flying.
Water / Dragon Arceus run bulky sets, with Recover and Toxic. Can stall Groudon to death.
Rayquaza is a very good counter. With Air Lock it can hit Groudon with a water-type move and hit hard with Earthquake. Also it is part of the "Let's laugh at Earthquake Group"
Primal Kyogre can switch in and OHKO Groudon with whatever move it has, although it is rendered useless under the Desolate Land.
There are just some counters to Groudon, now don't get me wrong, he's probably the best Pokemon in Ubers, behind Normal-Arceus of course. He won't go down easy, but most of these Pokemon can take it down, some even comfortably.
Hope I helped!