PokéBase - Pokémon Q&A
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Fishing chains are when you constantly fish with one of the Rod items. The more fish you get in a row, the higher your chance of finding a Shiny Pokemon becomes. The following things will break your chain:

  • Moving from your position. Once you start chain fishing do not move anywhere or your chain will be broken.
  • Pulling in the rod too early or too late.
  • Not getting a Pokemon on your rod. This happens naturally and is almost inevitable. However, if you lead your party with a Pokemon with the ability Suction Cups, you are guaranteed to get a Pokemon on your Rod, eliminating this from the list of things that could break your chain.

What you do in battles does not effect your chain; whether you catch the Pokemon, defeat it or run from it, the chain continues.

I also find that accessing a menu in the overworld breaks your chain, though this may be coincidental.

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Thanks I'll give it a try
No problem :)
Oh one more thing do you have to capture the pokemon or just defeat it.
Both will work; your actions in battle do not effect your chain at all. This means that you could run from every battle if you'd like :)
OK thanks again
It doesn't matter run kill it capture it really doesn't matter and I won't break your chain. So don't worry. Getting good at it will take time.
I have a question about it. If you close your 3ds system at any time during your chain will it break?
@Charizard: No problem.
@Carebears: I am not 100% sure about this. Though I am quite doubtful that going into Sleep Mode would end your chain as it hasn't been proven to do so and I see no reason why it would.
I was just wondering cause some sites say it is unknown and to avoid it and others don't say anything about it at all.

Thank you you really helped a lot!