PRTG Manual: IPv6
PRTG supports the IPv6 protocol for most sensor types. You can choose whether you want PRTG to query data from your network devices via an IPv4 or IPv6 connection. Indicate your preference in the Device Settings of each device. The sensors you add to the device will use the protocol you have indicated.
In the Outgoing IP Settings of the PRTG Administration Tool, you can additionally choose which IPv6 address will be used for outgoing monitoring requests. The the same option is also available for IPv4.
Not all sensor types are IPv6 compatible. You can see which sensors support IPv6 in the Add Sensor dialog. Incompatible sensors are not selectable on IPv6 devices.