RNA labeling is crucial for the study of RNA structure and metabolism. Herein we report N-6-allyladenosine (a(6)A) as a new small molecule for RNA labeling through both metabolic and enzyme-assisted manners. a(6)A behaves like A and can be metabolically incorporated into newly synthesized RNAs inside mammalian cells. We also show that human RNA N-6-methyladenosine (m(6)A) methyltransferases METTL3/METTL14 can work with a synthetic cofactor, namely allyl-SAM (S-adenosyl methionine with methyl replaced by allyl) in order to site-specifically install an allyl group to the N-6-position of A within specific sequence to generate a(6)A-labeled RNAs. The iodination of N-6-allyl group of a(6)A under mild buffer conditions spontaneously induces the formation of N-1,N-6-cyclized adenosine and creates mutations at its opposite site during complementary DNA synthesis of reverse transcription. The existing m(6)A in RNA is inert to methyltransferase-assisted allyl labeling, which offers a chance to differentiate m(6)A from A at individual RNA sites. Our work demonstrates a new method for RNA labeling, which could find applications in developing sequencing methods for nascent RNAs and RNA modifications.