In mammals, a subset of arginine tRNA isoacceptors are methylated in the anticodon loop by the METTL2 methyltransferase to form the 3-methylcytosine (m3C) modification. However, the mechanism by which METTL2 identifies specific arginine tRNAs for m3C formation as well as the biological role of m3C in mammals is unknown. Here, we show that human METTL2 forms a complex with DALR anticodon binding domain containing 3 (DALRD3) protein in order to recognize particular arginine tRNAs destined for m3C modification. Using biochemical reconstitution, we find that METTL2-DALDR3 complexes catalyze m3C formation in vitro that is dependent upon sequence elements specific to certain arginine tRNAs. Notably, DALRD3-deficient human cells exhibit nearly complete loss of the m3C modification in arginine tRNAs. These findings uncover an unexpected function for the DALRD3 protein in the targeting of distinct arginine tRNAs for m3C modification.