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What is the most efficient use of the Masuda Method?

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The way I currently do it - I bike back and forth on Route 7 gathering eggs and boxing them 5 at a time. When the box fills up, I go to Lumiose city and use hatching power 3 to burn through the 30 eggs.
Is there a more efficient way to do it?

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Your method is pretty much perfect, the only problem is you should use a Pokemon with Flame Body to make the eggs hatch faster, like Talonflame (it also gets Fly so it's extra convenient).

EDIT - also, the Oval Charm makes Pokemon breed faster.

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Thanks. I do use Talonflame and Oval charm, I just forgot to mention those.
Definitely use flame body.