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I was wondering as I read on a website but it didn't tell me.

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Here are some berries I know that are hard to get a hold of

Enigma Berry
Micle Berry
Custap Berry
Jaboca Berry
Rowap Berry
Kee Berry
Maranga Berry

There are also these super rare berries in R/S, but if you transfer them via Pal Park, they will become enigma berries.

Hope I helped!

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Dang, I took too long to answer
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Note: I am only listing the berries that you cannot get from berry patches, these berries may be available through catching wild Pokemon, contests.But I will include where you can get them if not from berry patches.

Cornn Berry | Berry master or Little Girl in Sootopolis City
Magost Berry | Berry master or Little Girl in Sootopolis City
Rabuta Berry | Berry master or Little Girl in Sootopolis City
Nomel Berry | Berry master or Little Girl in Sootopolis City
Spelon Berry | Tell the berry master's wife the special saying or beating hyper rank of a Contest and getting it from a fan
Pamtre Berry | Tell the berry master's wife the special saying or beating hyper rank of a Contest and getting it from a fan
Watmel Berry | Tell the berry master's wife the special saying or beating hyper rank of a Contest and getting it from a fan
Durin Berry | Tell the berry master's wife the special saying or beating hyper rank of a Contest and getting it from a fan
Belue Berry | Tell the berry master's wife the special saying or beating hyper rank of a Contest and getting it from a fan
Liechi Berry | Secret Pal who has the Berry Farmer skill
Ganlon Berry | Secret Pal who has the Berry Farmer skill
Salac Berry | ?
Petaya Berry | Secret Pal who has the Berry Farmer skill
Apicot Berry | Secret Pal who has the Berry Farmer skill
Lansat berry | Win 100 super battles in a row
Starf Berry | Win 200 super battles in a row
Enigma Berry | Special events
Micle Berry | Special events
Custap berry | Special events
Jaboca Berry | Special events
Rowap Berry | ?
Kee Berry | Secret Pal who has the Berry Farmer skill
Maranga Berry | Secret Pal who has the Berry Farmer skill
So, I would say the rarest ones are the special event only berries or the ? berries.
Hope I helped!
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