Three answers
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If you purchase packages - there is one for Atlantis coins that appears every Atlantis rises ( so far )
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If you are FTP , then it’s only buy those O. seahorses that randomly spawn during Atlantis stages Only . They drop a few coins on defeat.
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You can get them as possible drops in chests as well (titan/mission/raid chests ),
Edit : added @JonahTheBard input
Indeed you do get them as drops from chests , you are right .