Are Cisco IP phones compatible with Microsoft Lync Server? Is there any way to make them work together?
The direct answer to the first part of this question is no: Cisco IP phones are not directly compatible with Microsoft Lync Server. In other words, you cannot have a Cisco IP phone natively register with a Lync Front End Server. However, in regard to the second part of this question, Cisco IP phones can coexist with Lync phones with proper planning and design. There are various levels of coexistence. If an organization has Cisco Unified Communications Manager deployed as their IP-PBX for Cisco IP phones, it may be possible, depending on the software version, to create a SIP trunk (aka Direct SIP in Microsoft terminology) between CUCM and Lync Server. This Direct SIP connection will allow both Cisco IP phones and Lync clients and devices to communicate within the same organization without requiring a separate media gateway for transcoding.
Microsoft provides a list of supported Cisco IP-PBXes on the Infrastructure page of its Unified Communications Open Interoperability Program (UCOIP) website. Lync Server 2013 and Lync Server 2010 have both been tested with various software versions of CUCM. An excellent integration document is available at this site for Lync Server 2010 and CUCM. Cisco PBXes not listed on the UCOIP website may require the deployment of a separate SIP/CSTA gateway for Lync Server to be able to interoperate with the Cisco IP-PBX.
In addition to the native call control that exists both in CUCM and Lync Server, it is also possible to implement Remote Call Control (RCC). Cisco provides the Cisco Unified Presence server (CUPS) that will allow a Microsoft Lync client to send instructions to CUCM to control what happens on Cisco IP phones. Common examples include both Lync and Cisco IP phones ringing for an inbound call to both system and presence information; this would allow Available, Away and Busy statuses to be shared from Lync clients to the Cisco IP phone. Cisco has an integration guide available for CUPS 8.6 with Microsoft Lync Server for RCC. On the Lync Server side, Microsoft allows administrators to enable RCC for a Lync client. To clarify, the behavior of a Lync client enabled for RCC is somewhat different from that of a Lync client enabled for Enterprise Voice. For more detail, see Microsoft TechNet's articles, Planning for Remote Call Control and Deploying Remote Call Control.
See the response to the second part of this question: Does Microsoft offer IP phones?
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