I was reading a book called I-Boat Captain and it was about a Japanese sub captain in WWII. In it he lists the different sub losses that occured during the war in the Pacific and early in the war he lists a Russian sub that was lost in the Pacific. I was curious as to how the different branches of the service and different countries could tell who's submarine was who. For example how did a RAF pilot tell if he was seeing an Italian sub or an English sub on his radar or a Japanese army pilot tell a Russian sub from a Japanese submarine or Austrialian sub ? Did they have IFF codes as on aircraft ?

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Unfortunately No.
The Submariners had to hope that the Aircraft would recognize the differences in design between Allied submarines and Axis ones, or would take notice of any identification signals shown.
Also the Aircrew hopefully would have been warned where "friendly" submarines were operating, and would make checks before attacking, but I've spoken to a crewman off a British Submarine and he told me if they saw an aircraft, they would always dive before it got got close, even if it was an Allied aircraft. in his words " you couldn`t always trust the buggers not to attack"
Sadly, a number of Submarines were indeed lost in WW2 to "friendly fire".

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