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Swamy PSwamy P 

Email-2-Case Creates Multiple Cases on the Same Email Thread

Currently, we have email to case set up in UAT/PROD for salesforce.
When a user emails to, salesforce is configured to create a case automatically.
The problem arises when someone replies to the original email. It creates a new case.
Can anyone please investigate, if they reply to the original email it should not create a new case? Emails should append to the original case.

Thank you very much in advance!!
NagendraNagendra (Salesforce Developers) 
Hi Swamy,

May I suggest you please check with below link. Considering the above scenario there is an idea running on the success community for which you can upvote. Thanks,
Hi Swamy,

In case of Email-2-Case, Salesforce identifies the emails using the ThreadId, Thread Id is added to the email when agents reply back or in the autoresponder on case creation. 

In case enduser is again replying back to the original email, as it dont have ThreadId it is treated as new Email and case gets created. Try setting up autoresponder on case creation so that enduser replies to autoresponder and not from the original email. Else you can try writting a Inbound Email handler which will check exsiting cases and then create a new case if needed.