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For example Heracross and Pinsir are a duo since they both mega evolve, do not regularly evolve and are physical

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Duos, trios and quads in what respect though?
You can connect Rayquaza to Groudon and Kyogre easily, but at the same time you can also connect Rayquaza to Deoxys because they fought in the movie, both come from space and are legendary pokemon/ don't evolve.
You can connect all pokemon because of the fact that they are all pokemon.

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Best answer

I'm gonna post this answer because we have new Pokemon now.

Gen 1
Caterpie/Weedle
Ekans/Sandshrew
Nidoran Female/Nidoran Male
Clefairy/Jigglypuff
Vulpix/Growlithe
Oddish/Bellsprout (not counting Bellossom)
Meowth/Mankey
Grimer/Koffing
Krabby/Horsea (not counting Kingdra)
Hitmonlee/Hitmonchan
Lickitung/Tangela
Electabuzz/Magmar
Scyther/Pinsir (not counting Mega Scizor)
Vaporeon/Jolteon/Flareon
Omanyte/Kabuto
Articuno/Zapdos/Moltres (Lugia)

Gen 2
Ledyba/Spinarak
Espeon/Umbreon
Mukrow/Misdreavus
Gligar/Sneasel
Mantine/Skarmory (not counting Mantyke)
Raikou/Entei/Suicune (Ho-oh)
Lugia/Ho-oh

Gen 3
Silcoon/Cascoon
Lotad/Seedot
Sableye/Mawile
Plusle/Minun
Volbeat/Illumise
Carvahna/Numel
Zangoose/Seviper
Lunatone/Solrock
Lileep/Anorith
Shuppet/Duskull
Huntail/Gorebyss
Bagon/Beldum
Regirock/Regice/Registeel (Regigigas)
Latias/Latios
Kyogre/Groudon/Rayquaza (Deoxys)

Gen 4
Glameow/Stunky
Skorupi/Croagunk
Uxie/Mesprit/Azelf (Arceus)
Dialga/Palkia/Giratina (Arceus)
Phione/Manaphy

Gen 5
Pansage/Pansear/Panpour
Throh/Sawk
Sewaddle/Venipede
Cotonee/Petilil
Tirtouga/Archen
Gothita/Solosis
Karrablast/Shelmet
Rufflet/Vullaby
Heatmor/Durant
Cobalion/Terrakion/Virizion
Tornadus/Thundurus/Landorus/Enamorus1
Reshiram/Zekrom/Kyurem

Gen 6
Litleo/Espurr
Spritzee/Swirlix
Skrelp/Clauncher
Tyrunt/Amaura
Phantump/Pumpkaboo
Xerneas/Yveltal/Zygarde

Gen 7
Alolan Rattata/Yungoos
Oranguru/Passimian
Turtonator/Drampa
Tapu Koko/Tapu Lele/Tapu Bulu/Tapu Fini
Solgaleo/Lunala/Necrozma
Buzzwole/Pheromosa
Celesteela/Kartana
Stakataka/Blacephalon

Gen 8
Flapple/Appletun
Hatenna/Impidimp
Stonjourner/Eiscue
Dracozolt/Arctozolt/Dracovish/Arctovish
Zacian/Zamazenta
Regieleki/Regidrago
Glastrier/Spectrier/Calyrex

1: Enamorus was introduced in Gen 8 but belongs to the Kami group

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Enamorus is one of the Kami quartet, but it was introduced in Gen 8. Where would that be put?
6 votes

Pokémon Duos

Caterpie and Weedle and their Evolutionary Lines.

Ekans and Sandshrew and their Evolutionary Lines.

Nidoran♂ and Nidoran♀ and their Evolutionary Lines.

Clefairy and Jigglypuff and their Evolutionary Lines.

Vulpix and Growlithe and their Evolutionary Lines.

Meowth and Mankey and their Evolutionary Lines.

Grimer and Koffing and their Evolutionary Lines.

Shellder and Staryu and their Evolutionary Lines.

Hitmonlee and Hitmonchan

Electabuzz and Magmar and their Evolutionary Lines.

Omanyte and Kabuto and their Evolutionary Lines.

Mewtwo and Mew

Murkrow and Misdreavus and their Evolutionary Lines.

Ledyba and Spinarak and their Evolutionary Lines.

Tauros and Miltank

Espeon and Umbreon

Steelix and Scizor

Teddiursa and Phanpy and their Evolutionary Lines.

Skarmory and Mantine

Lugia and Ho-oh

Silcoon and Cascoon and their next Evolution.

Lotad and Seedot and their Evolutionary Lines.

Sableye and Mawile

Ninjask and Shedinja

Plusle and Minun

Volbeat and Illumise

Zangoose and Seviper

Solrock and Lunatone

Huntail and Gorebyss

Latias and Latios

Gardevoir and Gallade

Cranidos and Shieldon and their Evolutionary Lines.

Stunky and Glameow and their Evolutionary Lines.

Bonsly and Mime Jr. and their Evolutionary Lines.

Leafeon and Glaceon

Cresselia and Darkrai

Phione and Manaphy

Throh and Sawk

Sewaddle and Venipede and their Evolutionary Lines.

Cottonee and Petilil and their Evolutionary Lines.

Gothita and Solosis and their Evolutionary Lines.

Karrablast and Shelmet and their Evolutionary Lines.

Braviary and Mandibuzz and their Evolutionary Lines.

Heatmor and Durant

Spritzee and Slurpuff and their Evolutionary Lines.

Tyrunt and Amaura and their Evolutionary Lines.

Pokémon Trios

Hitmonlee, Hitmonchan and Hitmontop

Vaporeon, Jolteon and Flareon

Articuno, Zapdos and Moltres

Entei, Raikou and Suicune

Regirock, Regice and Registeel

Groudon, Kyogre and Rayquaza (Trio Master)

Dialga, Palkia and Giratina

Uxie, Mesprit and Azelf

Zekrom, Reshiram and Kyurem

Tornadus, Thundurus and Landorus (Trio Master)

Xerneas, Yveltal and Zygarde (Trio Master)

Pokémon Quads

Articuno, Zapdos, Moltres and Lugia (Master)

Entei, Raikou, Suicune and Ho-Oh (Master)

Regirock, Regice, Registeel and Regigigas (Master)

Dialga, Palkia, Giratina and Arceus (Master)

Uxie, Mesprit, Azelf and Arceus (Master)

Virizion, Terakion, Keldeo and Cobalion (Master)

Note: This list may be incomplete so if you feel I missed any Pokémon out feel free to leave a comment.

Source for Pokémon Duos.

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Thank you .
You're welcome :)
turtonator and drampa
solgaleo and lunala
In gens 1-3 magmar, electabuzz, and jynx were all part of a trio. However gen 4 onwards it became a duo between magmar and electabuzz because they didn’t want to give jynx more attention so they gave those 2 an evolution and baby. *Note all did get a baby in gen 2, but jynx didn’t get an evolution in gen 4*.
3 votes

I'm gonna assume you meant version exclusives the way it looks like, so here they are in no particualar order of appearance:

Generation 1 games (Red/Blue/Green/Yellow, FireRed/Leafgreen)
Magmar - Electabuzz
Vulpix - Growlithe
Oddish - Bellsprout
Meowth - Mankey
Sandshrew - Psyduck (somewhat, not sure)
Shellder - Staryu
Marill - Wooper
Murkrow - Misdreavus
Sneasel - Deliberd (not sure)
Slowpoke - Seel

Generation 2 games (Gold/Silver/Crystal, HeartGold/SoulSilver)
Spinarak - Ledyba
Teddiursa - Phanpy
Skarmory - Gligar
Omanyte - Kabuto
Lileep - Anorith
Gulpin - Baltoy

Generation 3 games (Ruby/Sapphire/Emerald, not counting OmegaRuby/AlphaSapphire of course)
Lotad - Seedot
Sableye - Mawile
Zangoose - Seviper
Lunatone - Solrock
Groudon - Kyogre
Deoxys Attack - Deoxys Defense (only emerald)

Generation 4 games (Diamond/Pearl/Platinum)
Scyther - Pinsir
Houndour - Poochyena
Larvitar - Bagon (perhaps)
Cranidos - Shieldon
Glameow - Stunky
Dialga - Palkia (Diamond and Pearl only)

Generation 5 games (Black/White, Black 2/White 2)
Caterpie - Weedle
Paras - Shroomish
Plusle - Minun
Gothita - Solosis
Rufflet - Vullaby
Tornadus - Thundurus
Zekrom - Reshiram
Numel - Spoink
Regice - Registeel
Latios - Latias
Skitty - Buneary
Kyurem W - Kyurem B

Generation 6 games (X/Y):
(not counting Mega Stones)
Pinsir - Heracross
Larvitar - Aron
Houndour - Electrike
Purrloin - Poochyena
Throh - Sawk
Spritzee - Swirlix
Skrelp - Clauncher
Xerneas - Yveltal

Here are some general duos/trios/quads of Legendary Pokemon:

Legendary Birds: Articuno, Zapdos, Moltres
Mew duo: Mew, Mewtwo
Legendary beasts: Raikou, Entei, Suicune
Tower duo: Ho-oh, Lugia
Legendary Golems: Regice, Registeel, Regirock. Regigigas
Eon duo: Latios, Latias
Weather trio: Groudon, Kyogre, Rayquaza
Lake Guardians: Azelf, Mesprit, Uxie
Creation trio: Dialga, Palkia, Giratina
Lunar duo: Cresselia, Darkrai
Sea Guardians: Phione, Manaphy
Swords of Justice: Cobalion, Terrakion, Virizion, Keldeo
Forces of Nature: Thundurus, Tornadus, Landorus
Tao trio: Reshiram, Zekrom, Kyurem
Mortality Duo: Xerneas, Yveltal

Hope I helped!

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^ under construction :P
Actually it's sandshrew and ekans
I meant like magby and elekid is what I meant but thanks anyway.
Its delibird and gligar. Just fyi.