On a system, can two CAN ports have the same CAN-ids?

If a device with two CAN ports have the same CAN-id, will this cause trouble? The networks are separated for some reason, but the "master" should be the same for both networks. Edit: Below the network topology.

("master")   CAN-BUS 0     +----------+
+----------+       |------->| CAN-ID 2 |
|          || CAN-ID 3 |
              CAN-BUS 1     +----------+

As what I now understand is that the CAN-id is set in software. If I play around with ifconfig you can not set the CAN-id. Instead, this is set when I want to generate CAN traffic through cangen:

CANID=1
ip link set can0 type can bitrate 125000
ip link set up can0
cangen can0 -I $CANID -L 8 -v