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Besides legendary Pokemon or traded Pokemon the rarest Pokemon in my opinion would be chimecho but its not very powerful. To catch it you must go onto the top of that mountain near the sarafi zone i forget the name sorry, but once you are on top search around in the grass until you find it, its very rare though.

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Q: What is the most rarest Pokemon on Pokemon emerald version and how do you get it?
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What are the rarest Pokemon in the Safari Zone?

AnswerThe rarest Pokemon in the Safari Zone differ with each version. Pokemon which are the hardest to catch will be listed here as the most rare. In Pokemon Red version, Scyther (a version exclusive) is a rare Pokemon. In Pokemon Blue, its counterpart is Pinsir. Both Pokemon have the same encounter rate in the Safari Zone. Across both Pokemon Red and Blue, Chansey is the rarest Pokemon while Kangaskhan, Tauros and Dratini are also rare, but with slightly higher encounter rates.The Pokemon Ruby and Sapphire Safari Zones do not appear to have version-exclusive Pokemon. Therefore, the rarest Pokemon are between the two games. Xatu, Heracross, Golduck and Pinsir all share the same catch rate and are therefore the rarest Pokemon for the Safari Zone.Pokemon Emerald has two new Safari Zone areas available once the player defeats the Elite Four. This results in Quagsire and Octillery becoming the most rare.The Sinnoh region's Great Marsh is the equivalent of the Safari Zone for Pokemon Diamond, Pearl and Platinum. It appears that Bidoof and Azuril are the rarest Pokemon found here. Their encounter rates are incredibly low compared to the other Pokemon available.With the new methods of capture available in Pokemon HeartGold and SoulSilver, it is near impossible to tell which Pokemon is the most rare. Customisable areas within the Safari Zone result in differing encounter rates. Even after a number of days, the encounter rate will change for a number of Pokemon, resulting in no one Pokemon being the most rare.

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