If my fuel is already registered with the Fuels and Fuel Additives program under 40 CFR Part 79, do I still need to register with the RFS2 program under 40 CFR Part 80?

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Yes. Even if your fuel or fuel additive is already registered under 40 CFR Part 79, there are additional registration requirements for parties regulated under the RFS2 program, as specified in 40 CFR 80.1450.