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I want to separate the software and physical part of an access point into two different equipments.

As a first step, I have installed hostapd in an Ubuntu server machine. How can we link hostapd to a physical wireless card located in another machine via ethernet?

P.S.: I have an Atheros chipset, AR9271, that supports monitor mode and works well as an AP with normal configuration of hostapd.

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You can't.

Hostapd needs low-level access to the wireless NIC, it's not something you can do over the network from a different machine (I don't see the point, and latency won't allow it anyway).

What you can do though is tell Hostapd to use a bridge (it has a specific configuration directive for this) that includes the Ethernet card of the server; that way you can put your DHCP and/or DNS server on another machine and connect the AP to it.

You can also configure Hostapd to authenticate using a remote Radius server so that user management is done on a different machine.

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