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I have network connecting with 500 users and 50 servers connecting different layer3 switches and layer2 switch. Can i run rstp in few switches and mstp on remaining switches.

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Yes, MSTP and RSTP interoperate. Practically, RSTP works like unconfigured MSTP with a single instance and region. RSTP peers are treated like MSTP peers in the common spanning tree (CST).

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RSTP and MSTP were developed from the ground up to make them work together. We can see MST as being a extension over RSTP. The MST BPDU is in fact and RSTP BPDU + some few additional things required to support several instance. So basically, from the perspective of an MST bridge, an RSTP peer looks like a different MST bridge in a different region. We don't find any issue running RSTP and MST both except of course that you will only be able to run a single instance (instance 0, the CIST) at the boundary between RSTP/MST. Hence hop count MST uses is only within a region. Between regions, MST uses the message age, just like RSTP.

Cisco will not support a real RSTP as defined in the IEEE. We only have Rapid-PVST, which is a proprietary version running one instance of RSTP per VLAN. The trick is that we don't need to support IEEE RSTP because MST is a superset of RSTP. Running MST with no region configuraiton is basically equivalent to running RSTP

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    "an RSTP peer looks like a different MST bridge in a different region" - no. An RSTP peer looks (almost) like a different MSTP bridge in the common spanning tree (CST).
    – Zac67
    Commented Sep 2, 2020 at 18:22

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