Can Confluence talk to two instances of JIRA?

Can our Confluence server version talk to two instances of JIRA (JIRA Developer and JIRA Service Desk) or would we need to start running to versions of Confluence? 

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It can, if in case they are two completely different instances. You will get the option to pick the instance for integration features like using the JIRA Issues macro.

We currently have JIRA Software Server version and in the process of evaluating JIRA Service Desk Cloud version, so my concern is having our Confluence Server talk to both a JIRA Server version and JIRA Cloud version simultaneously.  

It is surely possible. Connecting one more JIRA instance wouldn't affect the existing integration. Users will have to select the instance when they use macros and such.

Do you mean by JIRA Software? JIRA Service Desk sits on top of JIRA Core just like JIRA Software so technically, you just have to let your JIRA talk to a Confluence and both of them are already linked.

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